SoftGenetics - Software PowerTools for Genetic Analysis
 
       

 

Conferences and Papers

We are pleased and proud that leading researchers over the world choose our analytical tools to insure the accuracy of their research:

 

Mutation Surveyor citations
Mutation Explorer citations
GeneMarker citations
GeneMarker HID
citations

GeneMarker HTS citations
NextGENe citations
ChimerMarker citations

 

Citations of SoftGenetics NextGENe Software

 

2017

  1. A Whole Transcriptome Approach to Evaluating ReferenceGenes for Quantitative Gene Expression Studies: A Case Study in Mimulus
    Stanton, et al
    G3: Genes|Genomes|Genetics Early Online, published on March 3, 2017 as doi:10.1534/g3.116.038075 (Read the article)
  2. Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology
    DiBardino et al
    CytoJournal 2017, 14:7 (Read the article)
  3. A complex intragenic rearrangement of ERCC8 in Chinese siblings with Cockayne syndrome
    Xie, et al
    Sci Rep. 2017; 7: 44271. Published online 2017 Mar 23. doi: 10.1038/srep44271 (Read the article)
  4. Multiple gene variations contributed to congenital heart disease via GATA family transcriptional regulation
    Qian, et al
    Journal of Translational Medicine201715:69 DOI: 10.1186/s12967-017- 1173-0 (Read the article)
  5. Propionic Academia: Exome Sequencing Identified Novel Mutation in Exon 12 of PCCA Gene
    Khalesi, et al
    Journal of Medical Cases, ISSN 1923-4155 print, 1923-4163 online, Open Access Volume 8, Number 4, April 2017, pages 111-113 (Read the article)
  6. Myopia and Late-Onset Progressive Cone Dystrophy Associate to LVAVA/MVAVA Exon 3 Interchange Haplotypes of Opsin Genes on Chromosome X
    Orosz et al
    Investigative Ophthalmology & Visual Science March 2017, Vol.58, 1834-1842. doi:10.1167/iovs.16-21405 (Read the article)
  7. Live birth derived from oocyte spindle transfer to prevent mitochondrial disease
    Zhang, et al
    Reproductive BioMedicine Online, Volume 34, Issue 4, April 2017, Pages 361 – 368 (Read the article)
  8. A complex intragenic rearrangement of ERCC8 in Chinese siblings with Cockayne syndrome
    Xie, et al
    Scientific Reports 7 (1): 44271. doi:10.1038/srep44271. (Read the article)
  9. Confirmation of mutations in PROSC as a novel cause of vitamin B6-dependent epilepsy
    Pleck, et al
    Journal of Medical Genetics (Read the article)
  10. Frequent hypomorphic alleles account for a significant fraction of ABCA4 disease and distinguish it from age-related macular degeneration
    Zernant, et al
    Journal of Medical Genetics (Read the article)
  11. Linking newborn severe combined immunodeficiency screening with targeted exome sequencing: A case report
    Patel, et al
    The Journal of Allergy and Clinical Immunology (Read the article)
  12. Adaptive shaping of the behavioural and neuroendocrine phenotype during adolescence
    Zimmermann et al
    Proceedings of the Royal Society
    Published 15 February 2017.DOI: 10.1098/rspb.2016.2784 (Read the article)
  13. Whole exome sequencing reveals a mutation in ARMC9 as a cause of mental retardation, ptosis and polydactyly
    Kar et al (Read the article)
  14. Next-Generation Sequencing Approach in Methylation Analysis of HNF1B and GATA4 Genes: Searching for Biomarkers in Ovarian Cancer
    Bubancova et al
    International Journal of Molecular Sciences
  15. Identification of TAZ mutations in pediatric patients with cardiomyopathy by targeted next-generation sequencing in a Chinese cohort
    Wang et al
    Orphanet Journal of Rare Diseases 2017; 12: 26. (Read the article)

Familial atypical parkinsonism with rare variant in VPS35 and FBXO7 genes

Bartonikova, et al

Medicine (Baltimore)v.95(46); 2016 NovPMC5120934 (Read the article)

 

Cytology Sample Based Next-Generation Sequencing for Metastatic Melanoma: A Feasible and Useful Tool

Nomani, et al

Journal of the American Society of Crytopathology (Read the article)

 

Impact of external pneumatic compression target inflation pressure on transcriptome‐wide RNA expression in skeletal muscle

Martin, et al

Physiological Reports Published 24 November 2016 Vol. 4 no. e13029 DOI: 10.14814/phy2.13029 (Read the article)

 

Validation and implementation of a custom 21-gene panel next-generation sequencing assay for myeloid neoplasms

Loovers, et al (Read the article)

 

A novel germline POLE mutation causes an early onset cancer prone syndrome mimicking constitutional mismatch repair deficiency

Wimmer et al

Familial Cancer (2016). doi:10.1007/s10689-016- 9925-1 (Read the article)

 

A Multi-Institution Phase I Trial of Ruxolitinib in Patients with Chronic Myelomonocytic Leukemia (CMML)

Padron et al

Clinical Cancer Research

DOI: 10.1158/1078-0432.CCR- 15-2781 Published July 2016 (Read the article)

 

Simultaneous Expression of ABCA4 and GPR143 Mutations: A Complex Phenotypic Manifestation

Lee et al

IOVS June 2016 (Read the article)

 

Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis

Schenkel et al

The Journal of Molecular Diagnostics (Read the article)

 

Mitochondrial DNA Rearrangement Spectrum in Brain Tissue of Alzheimer’s Disease: Analysis of 13 Cases

Yucai Chen, Changsheng Liu, William Davis Parker, Hongyi Chen, Thomas G. Beach, Xinhua Liu, Geidy E. Serrano, Yanfen Lu, Jianjun Huang, Kunfang Yang, Chunmei Wang

Published: June 14, 2016 (Read the article)

 

CODAS Syndrome Is Associated with Mutations of LONP1, Encoding Mitochondrial AAA+ Lon Protease

Strauss et al (Read the article)

 

Analysis of PI3K/mTOR Pathway Biomarkers and Their Prognostic Value in Women with Hormone Receptor–Positive, HER2-Negative Early Breast Cancer

Azim, et al (Read the article)

 

Molecular Investigation of Sudden Cardia Death: The New York Experience

Barbara Simpson MD, PhD (Read the article)

 

Complex Camptosynpolydactyly and Mesoaxial synostotic syndactyly with phalangeal reduction are allelic disorders

Phadke, et al (Read the article)

 

Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome

Benjamin, et al (Read the article)

 

Prenatal diagnosis of complete maternal uniparental isodisomy of chromosome 4 in a fetus without congenital abnormality or inherited disease-associated variations
WeiQiang Liu, HuiMin Zhang, Jian Wang, GuoJiu Yu, WenJun Qiu, ZhiHua Li, Min Chen, Kwong Wai Choy and XiaoFang Sun (Read the article)

 

KRAS G12D mosaic mutation in a Chinese linear nevus sebaceous syndrome infant
Huijun Wang, Yanyan Qian, Bingbing Wu, Ping Zhang and Wenhao Zhou (Read the article)

 

Cost Effective Bioinformatics Pipeline for NGS Reporting of Clinically Relevant Cancer Genes Using the Ampliseq Cancer Hotspot Panel v2
Rebecca Stolarczyk, Keith Tomaszewicz, Xiuling Meng, Bruce A Woda, Lloyd M. Hutchinson, Ediz F. Cosar, Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA (Read the article)

 

Targeted Sequencing Identifies Associations Between IL7R-JAK Mutations And Epigenetic Modulators In T-Cell Acute Lymphoblastic Leukemia
Carmen Vicente, Claire Schwab, Michaël Broux, Ellen Geerdens, Sandrine Degryse, Sofie Demeyer, Idoya Lahortiga, Alannah Elliott, Lucy Chilton, Roberta La Starza, Cristina Mecucci, Peter Vandenberghe, Nicholas Goulden, Ajay Vora, Anthony V. Moorman, Jean Soulier, Christine J. Harrison, Emmanuelle Clappier, Jan Cools. Haematologica October 2015 100: 1301-1310; Doi:10.3324/haematol.2015.130179 (Read the article)

 

Leptin Receptor Somatic Mutations Are Frequent in HCV-Infected Cirrhotic Liver and Associated With Hepatocellular Carcinoma
Atsuyuki Ikeda, Takahiro Shimizu, Yuko Matsumoto, Yosuke Fujii, Yuji Eso, Tadashi Inuzuka, Aya Mizuguchi, Kazuharu Shimizu, Etsuro Hatano, Shinji Uemoto, Tsutomu Chiba, and Hiroyuki Marusawa (Read the article)

 

A custom software solution for forensic mtDNA analysis of MiSeq data
M. Holland, J. McElhoe, Forensic Sci. Int. Gene. Suppl. (2015) (Read the article)

 

Targeted Sequencing of the Mitochondrial Genome of Women at High Risk of Breast Cancer without Detectable Mutations in BRCA1/2
Sophie Blein, Laure Barjhoux, GENESIS investigators, Francesca Damiola, Marie-Gabrielle Dondon, Séverine Eon-Marchais, Morgane Marcou, Olivier Caron, Alain Lortholary, Bruno Buecher, Philippe Vennin†, Pascaline Berthet, Catherine Noguès, David G. Cox. Published: September 25, 2015 DOI: 10.1371/journal.pone.0136192 (Read the article)

 

Capture-based high-coverage NGS: a powerful tool to uncover a wide spectrum of mutation types
Jing Wang, Hui Yu, Victor Wei Zhang, Xia Tian, Yanming Feng, Guoli Wang, Elizabeth Gorman, Hao Wang, Richard E. Lutz, Eric S. Schmitt, Sandra Peacock & Lee-Jun Wong (Read the article)

 

Targeted sequencing identifies associations between IL7R-JAK mutations and epigenetic modulators in T-cell acute lymphoblastic leukemia
Carmen Vicente, Claire Schwab, Michaël Broux, Ellen Geerdens, Sandrine Degryse, Sofie Demeyer, Idoya Lahortiga, Alannah Elliott, Lucy Chilton, Roberta La Starza, Cristina Mecucci, Peter Vandenberghe, Nicholas Goulden, Ajay Vora, Anthony V. Moorman, Jean Soulier, Christine J. Harrison, Emmanuelle Clappier, Jan Cools. Haematologica October 2015 100: 1301-1310; doi:10.3324/haematol.2015.130179 (Read the article)

 

BMPER variants associated with a novel, attenuated subtype of diaphanospondylodysostosis
Zheyuan Zong, Susan Tees, Firoz Miyanji, Clarissa Fauth, Christopher Reilly, Elena Lopez, Stephen Tredwell, Yigal Paul Goldberg, Allen Delaney, Patrice Eydoux, Margot Van Allen and Anna Lehman (Read the article)

 

Use of Targeted Exome Sequencing for Molecular Diagnosis of Skeletal Disorders
Daniel L. Polla, Maria T. O. Cardoso, Mayara C. B. Silva, Isabela C. C. Cardoso, Cristina T. N. Medina, Rosenelle Araujo, Camila C. Fernandes, Alessandra M. M. Reis, Rosangela V. de Andrade, Rinaldo W. Pereira, Robert Pogue (Read the article)

 

Evidence for human transmission of amyloid-β pathology and cerebral amyloid angiopathy
Zane Jaunmuktane, Simon Mead,  Matthew Ellis, Jonathan D. F. Wadsworth,  Andrew J. Nicoll, Joanna Kenny, Francesca Launchbury, Jacqueline Linehan, Angela Richard-Loendt, A. Sarah Walker, Peter Rudge, John Collinge & Sebastian Brandner. AffiliationsContributionsCorresponding authors. Nature 525, 247–250 (10 September 2015) doi:10.1038/nature15369. Received 26 April 2015 Accepted 14 August 2015 Published online 09 September 2015 Updated online 11 September 2015 (Read the article)

 

Audio summaryUniversal Screening for Familial Hypercholesterolemia in Children
Gašper Klančar, BS, Urh Grošelj, MD, Jernej Kovač, PhD, Nevenka Bratanič, MD, Nataša Bratina, MD, Katarina Trebušak Podkrajšek, PhD, Tadej Battelino, MD doi:10.1016/j.jacc.2015.07.017 (Read the article)

Genetic heterogeneity in Cornelia de Lange syndrome (CdLS) and CdLS-like phenotypes with observed and predicted levels of mosaicism
Morad Ansari, Gemma Poke, Quentin Ferry, Kathleen Williamson, Roland Aldridge, Alison M Meynert, Hemant Bengani, Cheng Yee Chan, Hülya Kayserili, Şahin Avci, Raoul C M Hennekam, Anne K Lampe, Egbert Redeker, Tessa Homfray, Alison Ross, Marie Falkenberg Smeland, Sahar Mansour, Michael J Parker, Jacqueline A Cook, Miranda Splitt, Richard B Fisher, Alan Fryer, Alex C Magee, Andrew Wilkie, Angela Barnicoat, Angela F Brady, Nicola S Cooper, Catherine Mercer, Charu Deshpande, Christopher P Bennett, Daniela T Pilz, Deborah Ruddy, Deirdre Cilliers, Diana S Johnson, Dragana Josifova, Elisabeth Rosser, Elizabeth M Thompson, Emma Wakeling, Esther Kinning, Fiona Stewart, Frances Flinter, Katta M Girisha, Helen Cox, Helen V Firth, Helen Kingston, Jamie S Wee, Jane A Hurst, Jill Clayton-Smith, John Tolmie, Julie Vogt, Katrina Tatton–Brown, Kate Chandler, Katrina Prescott, Louise Wilson, Mahdiyeh Behnam, Meriel McEntagart, Rosemarie Davidson, Sally-Ann Lynch, Sanjay Sisodiya, Sarju G Mehta, Shane A McKee, Shehla Mohammed, Simon Holden, Soo-Mi Park, Susan E Holder,Victoria Harrison, Vivienne McConnell, Wayne K Lam, Andrew J Green, Dian Donnai, Maria Bitner-Glindzicz, Deirdre E Donnelly, Christoffer Nellåker, Martin S Taylor, David R FitzPatrick (Read the article)

Mutational analysis by next generation sequencing of gastric type dysplasia occurring in hyperplastic polyps of the stomach
Marcela Salomao, , Aesis M. Luna, Jorge L. Sepulveda, Antonia R. Sepulveda. Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY. Received 20 August 2015, Accepted 24 August 2015, Available online 29 August 2015 (Read the article)

Bohring–Opitz syndrome (BOS) with a new ASXL1 pathogenic variant: Review of the most prevalent molecular and phenotypic features of the syndrome
Silvana Beatriz Dangiolo, Ashley Wilson, Vaidehi Jobanputra and Kwame Anyane-Yeboa. Article first published online: 14 SEP 2015 DOI: 10.1002/ajmg.a.37342 (Read the article)

What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual
Lynsey K. Whitacre, Polyana C. Tizioto, JaeWoo Kim, Tad S. Sonstegard, Steven G. Schroeder, Leeson J. Alexander, Juan F. Medrano, Robert D. Schnabel, Jeremy F. Taylor, and Jared E. Decker (Read the article)

Analysis of mixtures using next generation sequencing of mitochondrial DNA hypervariable regions
Hanna Kim, Henry A. Erlich, Cassandra D. Calloway. (Read the article)

Molecular diagnostic approaches to CMs.
Cardiomyopathy 2015-new ESC guidelines on hypertrophic cardiomyopathy London, Great Britain, May 29, 2015
Mgr. Ema Ruszová Ph.D., Mgr. Marcela Chmelarová, Ph.D., Doc. MUDr. Miroslav Solar, Ph.D., MUDr. Jan Fridrich, MUDr. Mária Šenkeríková, Prof. MUDr. Vladimír Palicka, Csc. (Read the article)

Near-Infrared Autofluorescence: Its Relationship to Short-Wavelength Autofluorescence and Optical Coherence Tomography in Recessive Stargardt Disease
Vivienne C. Greenstein; Ari D. Schuman; Winston Lee; Tobias Duncker; Jana Zernant; Rando Allikmets; Donald C. Hood; Janet R. Sparrow (Read the article)

Uncovering the molecular pathogenesis of congenital hyperinsulinism by panel gene sequencing in 32 Chinese patients
Zi-chuan Fan, Jin-wen Ni, Lin Yang, Li-yuan Hu, Si-min Ma, Mei Mei, Bi-jun Sun, Hui-jun Wang and Wen-hao Zhou. (Read the article)

Association Studies Between European MtDNA Haplogroups And Risk Of Smokers Developing COPD: A Study In The ECLIPSE Cohort
Ruth J. Mayer , PhD, William Rumsey , PhD, Olga Derbeneva , PhD, Maria Lvova , MD, Dimitra Chalkia , PhD , Nicholas W. Locantore , PhD, Douglas C. Wallace , PhD. Publication Date: 2015 (Read the article)

Genomic Study of DNA Alteration Events Caused by Ionizing Radiation in Human Embryonic Stem Cells via Next-Generation Sequencing
Van Nguyen, Irina V. Panyutin, Igor G. Panyutin, and Ronald D. Neumann (Read the article)

Clinical impact and cost-effectiveness of whole exome sequencing as a diagnostic tool: a pediatric center’s experience
C. Alexander Valencia, Ammar Husami, Jennifer Holle, Judith A. Johnson, Yaping Qian, Abhinav Mathur, Chao Wei, Subba Rao Indugula, Fanggeng Zou, Haiying Meng, Lijun Wang, Xia Li, Rachel Fisher, Tony Tan, Amber Hogart Begtrup, Kathleen Collins, Katie A. Wusik, Derek Neilson, Thomas Burrow, Elizabeth Schorry, Robert Hopkin, Mehdi Keddache, John Barker Harley, Kenneth M. Kaufman and Kejian Zhang (Read the article)

Targeted sequencing identifies association between IL7R-JAK mutations and epigenetic modulators in T-cell acute lymphoblastic leukemia
Carmen Vicente, Claire Schwab, Michaël Broux, Ellen Geerdens, Sandrine Degryse, Sofie Demeyer, Idoya Lahortiga, Alannah Elliott, Lucy Chilton, Roberta La Starza, Cristina Mecucci, Peter Vandenberghe, Nicholas Goulden, Ajay Vora, Anthony V. Moorman, Jean Soulier, Christine J. Harrison, Emmanuelle Clappier, and Jan Cools (Read the article)

Integrated analysis of miRNA, gene, and pathway regulatory networks in hepatic cancer stem cells
Min Ding, Jiang Li, Yong Yu, Hui Liu, Zi Yan, Jinghan Wang and Qijun Qian (Read the article)

Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations
Xuewen Liu, Yuxia Jia, Mark B. Stoopler, Yufeng Shen, Haiying Cheng, Jinli Chen, Mahesh Mansukhani, Sanjay Koul, Balazs Halmos⇑ and Alain C. Borczuk (Read the article)

Increased Incidence of Mitochondrial Cytochrome C Oxidase 1 Gene Mutations in Patients with Primary Ovarian Insufficiency
Xiumei Zhen, Bailin Wu, Jian Wang, Cuiling Lu, Huafang Gao, Jie Qiao. Published: July 30, 2015 (Read the article)

Metabolic rescue in pluripotent cells from patients with mtDNA disease
Hong Ma, Clifford D. L. Folmes, Jun Wu, Robert Morey, Sergio Mora-Castilla, Alejandro Ocampo, Li Ma, Joanna Poulton, Xinjian Wang, Riffat Ahmed, Eunju Kang, Yeonmi Lee, Tomonari Hayama, Ying Li, Crystal Van Dyken, Nuria Marti Gutierrez, Rebecca Tippner-Hedges, Amy Koski, Nargiz Mitalipov, Paula Amato, Don P. Wolf, Taosheng Huang, Andre Terzic, Louise C. Laurent, Juan Carlos Izpisua Belmonte (Read the article)

Towards a Next-Generation Sequencing Diagnostic Service for Tumour Genotyping: A Comparison of Panels and Platforms
George J. Burghel, Carolyn D. Hurst, Christopher M. Watson, Phillip A. Chambers, Helen Dickinson, Paul Roberts, and Margaret A. Knowles (Read the article)

Validation of an NGS Approach for Diagnostic BRCA1/BRCA2 Mutation Testing.
Dacheva D, Dodova R, Popov I, Goranova T, Mitkova A, Mitev V, Kaneva R., Mol Diagn Ther. 2015 Apr;19(2):119-30. (Read the article)

Hereditary Breast/Ovarian Cancer: A systematic screening of DNA repair genes in 300 consecutive patients
Andrea Gehrig, Birgit Halliger-Keller, Clemens R. Müller; Department of Human Genetics, University of Würzburg, German (Read the article)

Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development
doi: 10.1002/path.4520 (Read the article)

 

Targeted re-sequencing of cancer-related genes from matched FFPE and fresh-frozen tumor samples using the Illumina sequencing platform
Bibikova et al, Cancer Research (Read the article)

 

A comprehensive next generation sequencing-based genetic testing strategy to improve diagnosis of inherited pheochromocytoma and paraganglioma.
Rattenberry et al, J Clin Endocrinol Metab. 2013 Jul;98(7):E1248-56. doi: 10.1210/jc.2013-1319. Epub 2013 May 10. (Read the article)

 

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
Boeva et al, Oxford Journals Science & Mathematics Bioinformatics Volume 30, Issue 24 Pp. 3443-3450 (Read the article)

 

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Benjamin B Green et al, BMC Genomics (Read the article)

 

Differential Expression of GNAS and KRAS Mutations in Pancreatic Cysts
Linda S Lee, Leona A Doyle, Jeffrey Houghton, Sachin Sah, Andrew M Bellizzi, Anna E Szafranska-Schwarzbach, James R Conner, Vivek Kadiyala, Shadeah L Suleiman, Peter A Banks, Bernard F Andruss, Darwin L Conwell. JOP. J Pancreas (Online) 2014 Nov 28; 15(6): 581-586 (Read the article)

 

Next Generation Diagnostics
Birgit Sikkema-Raddatz, Department of Genetics, University Medical Center Groningen, The Netherlands. (Read the article)

 

Validation of a Next-Generation Sequencing Cancer Panel for Clinical Mutation Profiling in Patients with Diffuse Large B-Cell Lymphoma (DLBCL)
James Stover Jr., PhD, BS, Vivek Yellore, PhD, Alison Miller, MS and Jeff P. Sharman, MD (Read the article)

 

The Whole Genome Sequence of a Jack Russell Terrier with Progressive Spinocerebellar Ataxia and Myokymia Contains a Homozygous Disease-Associated KCNJ10 Missense Mutation.
D. Gilliam1, J. R. Coates, G. S. Johnson, L. Hansen1, T. Mhlanga-Mutangadura, J. F. Taylor, G. C. Johnson, R. D. Schnabel, D. P. O'Brien (Read the article)

 

ION TORRENT NEURODEGENERATION GENE PANEL - TECHNICAL INFORMATION V1.0
NHS Lothian (Read the article)

 

Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq
Jennifer A. McElhoea, Mitchell M. Hollanda, Kateryna D. Makovab, Marcia Shu-Wei Sub, Ian M. Paulc, Christine H. Bakerd, Seth A. Faithd, Brian Young. Forensic Science International: Genetics (2014) (Read the article)

 

Germline mutations in the PAF1 complex gene ​CTR9 predispose to Wilms tumour
Sandra Hanks, et al. Nature Communications Article number: 4398 (Read the article)

 

Mutational analysis of serous ovarian cancer using Ion Torrent sequencing
Salome Masghati Oliver Dorigo, and Chintda Santisvkulvong. Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA (Read the article)

 

Evaluation of a new NGS method based on a custom AmpliSeq library and Ion Torrent PGM sequencing for the fast detection of genetic variations in cardiomyopathies.
Clin Chim Acta 2014 Jun 8;433:266-71. Epub 2014 Apr 8. Gilles Millat, Valérie Chanavat, Robert Rousson (Read the article)

 

Evaluation of a New High-Throughput Next-Generation Sequencing Method Based on a Custom AmpliSeq™ Library and Ion Torrent PGM™ Sequencing for the Rapid Detection of Genetic Variations in Long QT Syndrome.
Mol Diagn Ther 2014 Oct;18(5):533-9. Gilles Millat, Valérie Chanavat, Robert Rousson. Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, 69677, Bron Cedex, France. (Read the article)

 

Quantitative Fundus Autofluorescence Distinguishes ABCA4-Associated and Non–ABCA4-Associated Bull's-Eye Maculopathy
Tobias Duncker, MD, Stephen H. Tsang, MD, PhD, Winston Lee, MA, Jana Zernant, MS, Rando Allikmets, PhD, François C. Delori, PhD, Janet R. Sparrow, PhDemail.
Ophthalmology : October 03, 2014 (Read the article)

 

Clonal Expansion of Early to Mid-Life Mitochondrial DNA Point Mutations Drives Mitochondrial Dysfunction during Human Ageing
Laura C. Greaves mail, Marco Nooteboom, Joanna L. Elson, Helen A. L. Tuppen, Geoffrey A. Taylor, Daniel M. Commane, Ramesh P. Arasaradnam, Konstantin Khrapko, Robert W. Taylor, Thomas B. L. Kirkwood, John C. Mathers, Douglass M. Turnbull. Plos Genetics September 18, 2014DOI: 10.1371/journal.pgen.1004620 (Read the article)

 

ION TORRENT NEURODEGENERATION GENE PANEL - TECHNICAL
INFORMATION V1.0 NHS Lothian (Read the article)

 

Migrating partial seizures of infancy: delineation of the clinical and genetic features in a national patient cohort
Dr Amy McTague MBChB, Richard Appleton MBChB, Prof J Helen Cross PhD, Thomas S Jacques PhD, Esther Meyer PhD, Annapurna Poduri MD, Prof Ingrid Scheffer MD, Rachel Kneen MBChB, Manju A Kurian PhD. The Lancet, Volume 383, Page S14, 26 February 2014 doi:10.1016/S0140-6736(14)60277-4 (Read the article)

 

Genetic heterogeneity in Cornelia de Lange syndrome (CdLS) and CdLS-like phenotypes with observed and predicted levels of mosaicism
Morad Ansari, Gemma Poke, Quentin Ferry, Kathleen Williamson, Roland Aldridge, Alison M Meynert, Hemant Bengani, Cheng Yee Chan, Hülya Kayserili, Şahin Avci, Raoul C M Hennekam, Anne K Lampe, Egbert Redeker, Tessa Homfray, Alison Ross, Marie Falkenberg Smeland, Sahar Mansour, Michael J Parker, Jacqueline A Cook, Miranda Splitt, Richard B Fisher, Alan Fryer, Alex C Magee, Andrew Wilkie, Angela Barnicoat, Angela F Brady, Nicola S Cooper, Catherine Mercer, Charu Deshpande, Christopher P Bennett, Daniela T Pilz, Deborah Ruddy, Deirdre Cilliers, Diana S Johnson, Dragana Josifova, Elisabeth Rosser, Elizabeth M Thompson, Emma Wakeling, Esther Kinning, Fiona Stewart, Frances Flinter, Katta M Girisha, Helen Cox, Helen V Firth, Helen Kingston, Jamie S Wee, Jane A Hurst, Jill Clayton-Smith, John Tolmie, Julie Vogt, Katrina Tatton–Brown, Kate Chandler, Katrina Prescott, Louise Wilson, Mahdiyeh Behnam, Meriel McEntagart, Rosemarie Davidson, Sally-Ann Lynch, Sanjay Sisodiya, Sarju G Mehta, Shane A McKee, Shehla Mohammed, Simon Holden, Soo-Mi Park, Susan E Holder, Victoria Harrison, Vivienne McConnell, Wayne K Lam, Andrew J Green, Dian Donnai, Maria Bitner-Glindzicz, Deirdre E Donnelly, Christoffer Nellåker, Martin S Taylor, David R FitzPatrick (Read the article)

 

Animal Breeding in the Next-Generation Sequencing Era
Division of Animal Sciences, University of Missouri, Columbia, MO, USA. J.F. Taylor, J.E. Decker, and R.D. Schnabel (Read the article)

 

Fitness Impact and Stability of a Transgene Conferring Resistance to Dengue-2 Virus following Introgression into a Genetically Diverse Aedes aegypti Strain
Alexander W. E. Franz, Irma Sanchez-Vargas, Robyn R. Raban, William C. Black IV, Anthony A. James, Ken E. Olson (Read the article)

 

Necroptosis Drives Motor Neuron Death in Models of Both Sporadic and Familial ALS
Diane B. Re, Virginia Le Verche, Changhao Yu, Mackenzie W. Amoroso, Kristin A. Politi, Sudarshan Phani, Burcin Ikiz, Lucas Hoffmann, Martijn Koolen, Tetsuya Nagata, Dimitra Papadimitriou, Peter Nagy, Hiroshi Mitsumoto, Shingo Kariya, Hynek Wichterle, Christopher E. Henderson, and Serge Przedborski (Read the article)

 

Disease-related mutations among Caribbean Hispanics with familial dementia
Joseph H. Lee1, Amanda Kahn, Rong Cheng, Christiane Reitz, Badri Vardarajan, Rafael Lantigua, Martin Medrano, Ivonne Z. Jimenez-Velazquez, Jennifer Williamson, Peter Nagy, and Richard Mayeux (Read the article)

 

Improved molecular diagnosis by the detection of exonic deletions with target gene capture and deep sequencing
Yanming Feng PhD, David Chen MS, Guo-Li Wang PhD, Victor Wei Zhang MD, PhD & Lee-Jun C. Wong PhD (Read the article)

 

SIMULTANEOUS DETECTION OF KRAS, NRAS ANDBRAF HOTSPOT MUTATIONS ON ION TORRENT PGM PLATFORM
Ann Oncol (2014) 25 (suppl 2): ii67 (Read the article)

 

NGS Nominated CELA1, HSPG2, and KCNK5 as Candidate Genes for Predisposition to Balkan Endemic Nephropathy
D. Toncheva, M. Mihailova-Hristova, R. Vazharova, R. Staneva, S. Karachanak, P. Dimitrov, V. Simeonov, S. Ivanov, L. Balabanski, D. Serbezov, M. Malinov, V. Stefanovic, R. Cukuranovic, M. Polenakovic, L. Jankovic-Velickovic, V. Djordjevic, T. Jevtovic-Stoimenov, D. Plaseska-Karanfilska, A. Galabov, V. Djonov, and I. Dimova
BioMed Research International, Volume 2014 (2014), Article ID 920723, 7 pages (Read the article)

 

Accumulation of Somatic Mutations in TP53 in Gastric Epithelium With Helicobacter pylori Infection.
Takahiro Shimizu, Hiroyuki Marusawa, Yuko Matsumoto, Tadashi Inuzuka, Atsuyuki Ikeda, Yosuke Fujii, Sachiko Minamiguchi, Shin’ichi Miyamoto, Tadayuki Kou, Yoshiharu Sakai, Jean E. Crabtree, Tsutomu Chiba; April 28, 2014 (Read the article)

 

Mung Bean Nuclease Treatment Increases Capture Specificity of Microdroplet-PCR Based Targeted DNA Enrichment
Zhenming Yu mail, Kajia Cao, Tanya Tischler, Catherine A. Stolle, Avni B. Santani, Published: July 24, 2014 (Read the article)

 

Germline mutations in the PAF1 complex gene ​CTR9 predispose to Wilms tumour
Sandra Hanks, Elizabeth R. Perdeaux, Sheila Seal, Elise Ruark, Shazia S. Mahamdallie, Anne Murray, Emma Ramsay, Silvana Del Vecchio Duarte, Anna Zachariou, Bianca de Souza, Margaret Warren-Perry, Anna Elliott, Alan Davidson, Helen Price, Charles Stiller, Kathy Pritchard-Jones & Nazneen Rahman (Read the article)

 

Assessing Deep Sequencing Technology for Human Forensic Mitochondrial DNA Analysis
Mark R. Wilson. Ph.D., July 2014 (Read the article)

 

Evaluation of a new NGS method based on a custom AmpliSeq library and Ion Torrent PGM sequencing for the fast detection of genetic variations in cardiomyopathies.
Gilles Millata, Valerie Chanavata, Robert Roussona (Read the article)

  1. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities.
    Lin X, Tang W, Ahmad S, Lu J, Colby CC, Zhu J, Yu Q. (Read the article)

  2. Identification of Genes for Childhood Heritable Diseases
    Annual Review of Medicine, Vol. 65: 19-31 DOI: 10.1146/annurev-med-101712-122108
    Kym M. Boycott, David A. Dyment, Sarah L. Sawyer, Megan R. Vanstone, and Chandree L. Beaulieu (Read the article)

  3. Repurposing CRISPR/Cas9 for in situ functional assays
    Abba Malina, John R. Mills, Regina Cencic, et al. (Read the article)

  4. The Development and Validation of a Next Generation Sequencing Panel for Skeletal Dysplasias
    Monica J. Basehore, Stephen McGee, Katharine Kubiak, Kellie King, Jamie Butler, Jennifer A. Lee, Julie R. Jones, and Michael J. Friez (View the poster)

  5. Genotyping of Fanconi Anemia Patients by Whole Exome Sequencing: Advantages and ChallengesKerstin Knies, Beatrice Schuster, Najim Ameziane,. Martin Rooimans,Thomas Bettecken,,Johan de Winter, Detlev Schindler (Read the article)

  6. SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.)Antonio Leonforte, Shimna Sudheesh, Noel OI Cogan, Philip A Salisbury, Marc E Nicolas, Michael Materne, John W Forster and Sukhjiwan Kaur (Read the article)

  7. A Missense Mutation in the Alpha-Actinin 1 Gene (ACTN1) Is the Cause of Autosomal Dominant Macrothrombocytopenia in a Large French Family
    Paul Guéguen mail, Karen Rouault, Jian-Min Chen, Odile Raguénès, Yann FichouElisabeth Hardy, Eric Gobin, Brigitte Pan-petesch, Mathieu Kerbiriou, Pascal Trouvé, Pascale Marcorelles, Jean-francois Abgrall, Cédric Le Maréchal, Claude Férec (Read the article)

  8. A mutation in the serine protease TMPRSS4 in a novel pediatric neurodegenerative disorder
    Piya Lahiry Lemuel Racacho, Jian Wang, John F Robinson, Gregory B Gloor, C Anthony Rupar, Victoria M Siu, Dennis E Bulman and Robert A Hegele; Lahiry et al. Orphanet Journal of Rare Diseases 2013, 8:126 (Read the article)

  9. Streamlined Ion Torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model
    Tarabeux J, Zeitouni B, Moncoutier V, Tenreiro H, Abidallah K, Lair S, Legoix-Né P, Leroy Q, Rouleau E, Golmard L, Barillot E, Stern MH, Rio-Frio T, Stoppa-Lyonnet D, Houdayer C. (Read the article)

  10. Dynamics of defective hepatitis C virus clones in reinfected liver grafts in liver transplant recipients; ultra-deep sequencing analysis
    Shigeru Ohtsuru1, Yoshihide Ueda, Hiroyuki Marusawa, Tadashi Inuzuka, Norihiro Nishijima, Akihiro Nasu, Kazuharu Shimizu, Kaoru Koike, Shinji Uemoto and Tsutomu Chiba (Read the article)

  11. Characterization of NIST Standard Reference Materials by Next Generation Sequencing
    Kevin M. Kiesler and Peter M. Vallone (View the poster)

  12. A mutation in the serine protease TMPRSS4 in a novel pediatric neurodegenerative disorder
    Piya Lahiry, et al (Read the article)

  13. Next-generation sequencing for disorders of low and high bone mineral density
    Sule et al Osteoporos Int. 2013 August; 24(8): 2253-2259.

  14. Mutations in GDP-Mannose Pyrophosphorylase B Cause Congenital and Limb-Girdle Muscular Dystrophies Associated with Hypoglycosylation of a-Dystroglycan
    Carss et al The American Journal of Human Genetics (2013) (Read the article)

  15. Short Read (Next-gen) Sequencing: A Tutorial with Cardiomyopathy Diagnostics as an Exemplar
    1. Jaya Punetha and Eric P. Hoffman (Read the article)

  16. Towards Sustained Silencing of Her2/neu in Cancer by Epigenetic Editing
    Fahimeh Falahi, Christian Huisman, Hinke G. Kazemier, Van der Vlies Pieter, Klaas Kok, Geke A.P. Hospers, and Marianne G. Rots (Read the article)

  17. A comprehensive next generation sequencing based genetic testing strategy to improve diagnosis of inherited pheochromocytoma and paraganglioma Rattenberry et al (Read the article)

  18. Unique X-linked familial FSGS with co-segregating heart block disorder is associated with a mutation in the NXF5 gene. Esposito T, Lea RA, Maher BH, Moses D, Cox HC, Magliocca S, Angius A, Nyholt DR, Titus T, Kay T, Gray NA, Rastaldi MP, Parnham A, Gianfrancesco F, Griffiths LR. (Read the article)

  19. Migrating partial seizures of infancy: expansion of the electroclinical, radiological and pathological disease spectrum McTague et al, Brain 2013: 136; 1578-1591

  20. Genome-wide dissection of globally emergent multi-drug resistant serotype 19A Streptococcus pneumonia Pillai et al (Read the article)

  21. Migrating partial seizures of infancy: expansion of the electroclinical, radiological and pathological disease spectrumAmy McTague, Richard Appleton, Shivaram Avula, J. Helen Cross, Mary D. King, Thomas S. Jacques, Sanjay Bhate, Anthony Cronin, Andrew Curran, Archana Desurkar, Michael A. Farrell, Elaine Hughes, Rosalind Jefferson, Karine Lascelles, John Livingston, Esther Meyer, Ailsa McLellan, Annapurna Poduri, Ingrid E. Scheffer, Stefan Spinty, Manju A. Kurian and Rachel Kneen (Read the article)

  22. Metabolic Adaptation to Chronic Inhibition of Mitochondrial Protein Synthesis in Acute Myeloid Leukemia Cells
    Bozhena Jhas, Shrivani Sriskanthadevan, Marko Skrtic, Mahadeo A. Sukhai, Veronique Voisin, Yulia Jitkova, Marcela Gronda,Rose Hurren, Rob C. Laister, Gary D. Bader, Mark D. Minden, Aaron D. Schimmer (Read the article)

  23. Role of Gα(olf) in Familial and Sporadic Adult-Onset Primary DystoniaSatya R. Vemula, Andreas Puschmann, Jianfeng Xiao,Yu Zhao,Monika Rudziñska,Karen P. Frei,Daniel D. Truong,Zbigniew K. Wszolek  andMark S. LeDoux (Read the article)

  24. Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia
    Mark E Samuels, et al; J Med Genet doi:10.1136/jmedgenet-2012-101483 (Read the article)

  25. Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations
    Ephrem LH Chin, Cristina da Silva, Madhuri Hegde (Read the article)

  26. Pathogenic mutations in two families with congenital cataract identified with whole-exome sequencingYukiko Kondo, Hirotomo Saitsu, Toshinobu Miyamoto, Byung Joo Lee, Kiyomi Nishiyama, Mitsuko Nakashima, Yoshinori Tsurusaki, Hiroshi Doi, Noriko Miyake, Jeong Hun Kim, Young Suk Yu, Naomichi MatsumotoMolecular Vision 2013; 19:384-389 (Read the article)

  27. Recessive mutations in EPG5 cause Vici syndrome, a multisystem disorder with defective autophagy
    Thomas Cullup, Ay Lin Kho, Carlo Dionisi-Vici, Birgit Brandmeier, Frances Smith, Zoe Urry, Michael A Simpson, Shu Yau, Enrico Bertini, Verity McClelland, Mohammed Al-Owain, Stefan Koelker, Christian Koerner, Georg F Hoffmann, Frits A Wijburg, Amber E ten Hoedt, R Curtis Rogers, David Manchester, Rie Miyata, Masaharu Hayashi, Elizabeth Said, Doriette Soler, Peter M Kroisel, Christian Windpassinger, Francis M Filloux et al. (Read the article)

  28. SRY mutation analysis by next generation (deep) sequencing in a cohort of chromosomal Disorders of Sex Development (DSD) patients with a mosaic karyotype BMC Medical Genetics 2012, 13:108 doi:10.1186/1471-2350-13-108 (Read the article)

  29. Genetics: Advance Online Publication, published on November 19, 2012 as 10.1534/genetics.112.142299
    (Read the article)

  30. Mutation Analysis of BRCA1 , BRCA2 , PALB2 and BRD7 in a Hospital-Based Series of German Patients with Triple- Negative Breast Cancer (Read the article)

  31. Identifying the genetic cause of primary immunodeficiency diseases (PID): Development of a next generation sequencing (NGS) approach for routine diagnostics. S. C. Drury, C. Bacchelli, S. Bibi, F. McKay, L. Jenkins, H. B. Gaspar, C. M. Cale, K. C. Gilmour, N. J. Lench; 1) NE Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, London, United Kingdom; 2) GOSgene, UCL Institute of Child Health, 30 Guilford Street, London, United Kingdom; 3) Department of Immunology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom. (Read the article)

  32. TMEM237 Is Mutated in Individuals with a Joubert Syndrome Related Disorder and Expands the Role of the TMEM Family at the Ciliary Transition Zone Lijia Huang, Katarzyna Szymanska, Victor L. Jensen, Andreas R. Janecke, A. Micheil Innes, Erica E. Davis, Patrick Frosk, Chunmei Li, Jason R. Willer, Bernard N. Chodirker, Cheryl R. Greenberg, D. Ross McLeod, Francois P. Bernier, Albert E. Chudley, Thomas Müller, Mohammad Shboul, Clare V. Logan, Catrina M. Loucks, Chandree L. Beaulieu, Rachel V. Bowie, Sandra M. Bell, Jonathan Adkins, Freddi I. Zuniga, Kevin D. Ross, Jian Wang, Matthew R. Ban, Christian Becker, Peter Nürnberg, Stuart Douglas, Cheryl M. Craft, Marie-Andree Akimenko, Robert A. Hegele, Carole Ober, Gerd Utermann, Hanno J. Bolz, Dennis E. Bulman, Nicholas Katsanis, Oliver E. Blacque, Dan Doherty, Jillian S. Parboosingh, Michel R. Leroux, [low asterisk] Colin A. Johnson, and Kym M. Boycott, (Read the article)

  33. Dynamics of Hepatitis B Virus Quasispecies in Association with Nucleos(t)ide Analogue Treatment Determined by Ultra-Deep Sequencing Norihiro Nishijima, Hiroyuki Marusawa, Yoshihide Ueda, Ken Takahashi, Akihiro Nasu, Yukio Osaki, Tadayuki Kou, Shujiro Yazumi, Takeshi Fujiwara, Soken Tsuchiya, Kazuharu Shimizu, Shinji Uemoto, and Tsutomu Chiba (Read the article)

  34. Comprehensive 1-Step Molecular Analyses of Mitochondrial Genome by Massively Parallel Sequencing Wei Zhang,,Hong Cui, and Lee-Jun C. Wong (Read the article)

  35. Whole genome sequencing reveals a deletion of the last exon of FAN1 in Basenji dogs with adult-onset Fanconi syndrome. G. S. Johnson, F. H. Farias, T. Mhlanga-Mutangadura, J. F. Taylor, D. P. O'Brien, R. D. Schnabel; 1) Department of Veterinary Pathobiology, University of Missouri, Columbia, MO; 2) Division of Animal Sciences, University of Missouri, Columbia, MO; 3) Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO. (Read the article)

  36. Empowering a clinical genetic setting through the introduction of whole exome sequencing in prenatal and postnatal investigations. C. Pangalos, B. Hagnefelt, Z. Agioutantis, C. Konialis; 1) Clinical Genetics, InterGenetics -Diagnostic Genetic Center, Athens, Greece; 2) Molecular Genetics, InterGenetics -Diagnostic Genetic Center, Athens, Greece; 3) Mineral Resources Engineering, Technical University of Crete, Hania, Greece. (Read the article)

  37. Enhanced detection of low-level mosaic mutations in RB1 gene in Sporadic Unilateral RB by Ion Torrent semiconductor sequencing: Risk of second cancer. Z. Chen, S. Walther, K. Moran, D. Gerhart, T. Ganguly, A. Ganguly; 1) Genetic Diagnostic Laboratory, Department of Genetics, University of Pennsylvania, Philadelphia, PA; 2) DNA Sequencing Facility, Department of Genetics, Perelman school of Medicine, University of Pennsylvania. (Read the article)

  38. Rapid Detection of the ACMG/ACOG-Recommended 23 CFTR Disease-Causing Mutations Using Ion Torrent Semiconductor Sequencing. Aaron M. Elliott, Joy Radecki, Bellal Moghis, Xiang Li, and Anja Kammesheidt (Read the article)

  39. Germline mutations in the oncogene EZH2 cause Weaver syndrome and increased human height
    Katrina Tatton-Brown, Sandra Hanks, Elise Ruark, Anna Zachariou, Silvana Del Vecchio Duarte, Emma Ramsay, Katie Snape, Anne Murray, Elizabeth R Perdeaux, Sheila Seal, Chey Loveday, Siddharth Banka, Carol Clericuzio, Frances Flinter, Alex Magee, Vivienne McConnell, Michael Patton, Wolfgang Raith, Julia Rankin, Miranda Splitt, Volker Strenger, Clare Taylor, Patricia Wheeler, I Karen Temple, Trevor Cole, The Childhood Overgrowth Collaboration, Jenny Douglas, and Nazneen Rahman (Read the article)

  40. Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb) Melanie L Hand, Noel Oi Cogan,and John W Forstercorresponding author (Read the article)

  41. Gene Expression Profiling of Liver Cancer Stem Cells by RNA-SequencingDavid W. Y. Ho,#1 Zhen Fan Yang, Kang Yi, Chi Tat Lam, Michael N. P. Ng, Wan Ching Yu, Joyce Lau, Timothy Wan,1 Xiaoqi Wang, Zhixiang Yan, Hang Liu, Yong Zhang, and Sheung Tat Fan (Read the article)

  42. Design and Implementation of Next Generation Sequencing Diagnostic Services for Inherited Colorectal Cancer
    Kimberley Reay, Danielle Crompton, Victoria Lindley, Richard Barber, Fiona Macdonald and Yvonne Wallis
    The West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, B15 2TG (Read the article)

  43. A Low-Cost Exon Capture Method Suitable for Large-Scale Screening of Genetic Deafness by the Massively-Parallel Sequencing Approach
    Wenxue Tang, Dong Qian, Shoeb Ahmad, Douglas Mattox, N. Wendell Todd, Harrison Han, Shouting Huang, Yuhua Li, Yunfeng Wang, Huawei Li, and Xi Lin
    Genetic Testing and Molecular Biomarkers. null, Vol. 0, No. 0
    (Read the article)

  44. Exome sequencing in a family with an X-linked lethal malformation syndrome: clinical consequences of hemizygous truncating OFD1 mutations in male patients
    Yoshinori Tsurusaki1, Tomoki Kosho, Kiyoshi Hatasaki, Yoko Narumi, Keiko Wakui2, Yoshimitsu Fukushima, Hiroshi Doi, Hirotomo Saitsu, Noriko Miyake, Naomichi Matsumoto
    DOI: 10.1111/j.1399-0004.2012.01885.x
    (Read the article)

  45. Validation and Implementation of a 62-Gene Next Generation Sequencing Panel for Syndromic Autism: Experience from a Clinical Diagnostic Laboratory
    Julie R Jones1, Monica J Basehore1, Stephen McGee1, Amanda Lindy1, Kristen J Champion1,
    Christin D Collins2, Madhuri Hegde2, Michael J Friez1
    1Greenwood Genetic Center, Greenwood, SC 2Emory Genetics Laboratory, Decatur, GA
    (Read the article)

  46. Targeted re-sequencing of cancer-related genes from matched FFPE and Fresh-Frozen tumor samples using the Illumina sequencing platform
    Marina Bibikova1, Jeremy Chien2, Vincent Ho1, Craig April1, Sarah Munchel1, Joseph Cottrell1, Samantha Cooper1, Russell Grocock1, Fiona Nielsen1, Yaman Tarabishy2, Daniel Visscher2, Megan Manion3, Jonathan Liu3, Eric Wieben2, Lynn Hartmann2, Kim Kalli2, Viji Shridhar 2, and Jian-Bing Fan1. 1Illumina, Inc., San Diego, California; 2Mayo Clinic, Rochester, Minnesota; 3Softgenetics, LLC, State College, Pennsylvania (Read the article)

  47. Identification of Gene Mutations in Autosomal Dominant Polycystic Kidney Disease through Targeted Resequencing Sandro Rossetti,* Katharina Hopp,† Robert A. Sikkink,‡ Jamie L. Sundsbak,* Yean Kit Lee,‡
    Vickie Kubly,* Bruce W. Eckloff,‡ Christopher J. Ward,* Christopher G. Winearls,§ Vicente E. Torres,* and Peter C. Harris* (Read the article)
    *Division of Nephrology and Hypertension, †Mayo Graduate School, and ‡Advanced Genomics Technology Center, Mayo Clinic, Rochester

  48. Whole Exome Sequencing in a Random Sample of North American Women with Leiomyomas Identifies MED12 Mutations in Majority of Uterine Leiomyomas Megan M. McGuire, Alexander Yatsenko, Lori Hoffner1, Mirka Jones, Urvashi Surti, Aleksandar Rajkovic (Read the article)

  49. A Novel Strategy For Fast And Cost-effective Mutation Detection In Retinitis Pigmentosa Genes Using Next Generation Sequencing
    Ralph J. Florijn, Renate C. Zekveld-Vroon1, Arne Bakker1, Martin A. Haagmans, Jaroslav Skokan1, Mary J. van Schooneveld, Olaf R. Mook2, Arthur A. Bergen1. 1Molecular Ophthalmogenetics, Netherlands Inst for Neuroscience, Amsterdam, The Netherlands; 2Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. (Read the article)

  50. Transgene Silencing and Transgene-Derived siRNA Production in Tobacco Plants Homozygous for an Introduced AtMYB90 Construct
    Jeff Velten1*, Cahid Cakir1, Eunseog Youn2, Junping Chen1, Christopher I. Cazzonelli3
    1 United States Department of Agriculture - Agricultural Research Service, Lubbock, Texas, United States of America, 2 Department of Computer Science, Texas Tech University, Lubbock, Texas, United States of America, 3 Australian Research Council - Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
    (Read the article)

  51. Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis
    Frauke Coppieters, Bram De Wilde, Steve Lefever, Ellen De Meester, Nina De Rocker, Caroline Van Cauwenbergh, Filip Pattyn, Françoise Meire, Bart P. Leroy, Jan Hellemans, Jo Vandesompele and Elfride De Baere (Read the article)

  52. An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia
    Cristina Dias Murat Sincan, Praveen F. Cherukuri, Rosemarie Rupps, Yan Huang, Hannah Briemberg, Kathryn Selby, James C. Mullikin for the NISC Comparative Sequencing Program, Thomas C. Markello, David R. Adams, William A. Gahl, Cornelius F. Boerkoel, (Read the article)

  53. Applications of next-generation sequencing in plant biology
    Ashley N. Egan, Jessica Schlueter and David M. Spooner (Read the article)

  54. DDOST Mutations Identified by Whole-Exome Sequencing Are Implicated in Congenital Disorders of Glycosylation
    Melanie A. Jones, Bobby G. Ng, Shruti Bhide, Ephrem Chin, Devin Rhodenizer, Ping He, Marie-Estelle Losfeld, Miao He, Kimiyo Raymond3, Gerard Berry, Hudson H. Freeze and Madhuri R. Hegde (Read the article)

  55. Mutations in CIZ1 cause adult-onset primary cervical dystonia
    Jianfeng Xiao MD, PhD, Ryan J. Uitti MD, Yu Zhao MD, PhD, Satya R. Vemula PhD, Joel S. Perlmutter MD, Zbigniew K. Wszolek MD, Demetrius M. Maraganore MD, Georg Auburger Dr. Med, Barbara Leube Dr. Med, Katja Lehnhoff PhD, Mark S. LeDoux MD, PhD (Read the article)

  56. Single Molecule Sequencing of Free DNA from Maternal Plasma for Noninvasive Trisomy 21 Detection (Read the article)

  57. Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis Sequence analysis was carried out with the NextGENe software v2.00 (SoftGenetics, LLC, State College, PA). Reads with a median quality score <20 or with ambiguous nucleotide calls (N ≥ 3) were removed. Subsequently ...(Read the article)

  58. Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation Jones, Melanie A. PhD; Bhide, Shruti MS; Chin, Ephrem MB(ASCP), QLC; Ng, Bobby G. BS; Rhodenizer, Devin BS; Zhang, Victor W. MD, PhD; Sun, Jessica J. MS; Tanner, Alice PhD, MS; Freeze, Hudson H. PhD; Hegde, Madhuri R. PhD, FACMG (Read the article)

  59. Derivation and feeder-free propagation of human embryonic stem cells under xeno-free conditions Dusko Ilic, Emma Stephenson, Victoria Wood, Laureen Jacquet, Danielle Stevenson, Anastasia Petrova, Neli Kadeva, Stefano Codognotto1, Heema Patel, Maxine Semple, Glenda Cornwell, Caroline Ogilvie & Peter Braude (Read the article)

  60. Fast and Cost-Effective Mining of Microsatellite Markers Using NGS Technology: An Example of a Korean Water Deer Hydropotes inermis argyropus Jeong-Nam Yu, Changman Won, Jumin Jun,YoungWoon Lim, Myounghai Kwak (Read the article)

  61. Ion AmpliSeq™ Cancer Panel (Read the article)

  62. UNIT 19.8 Next Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy (Read the article)

  63. Genetic Heterogeneity of Hepatitis C Virus in Association with Antiviral Therapy Determined by Ultra-Deep Sequencing (Read the article)

  64. Exome Sequencing Reveals a Homozygous SYT14 Mutation in Adult-Onset, Autosomal-Recessive Spinocerebellar Ataxia with Psychomotor Retardation (Read the article)

  65. The Parasitic Plant Genome Project: New Tools for Understanding the Biology of Orobanche and Striga (Read the article)

  66. A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: Targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population (Read the article)

  67. MED12, the Mediator Complex Subunit 12 Gene, Is Mutated at High Frequency in Uterine Leiomyomas (Read the article)

  68. Transcriptome Fingerprinting Analysis: An Approach to Explore Gene Expression Patterns in Marine Microbial Communities (Read the article)

  69. Gene flow increases fitness at the warm edge of a species' range (Read the article)

  70. Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma (Read the article)

  71. Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system (Read the article)

  72. Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations (Read the article)

  73. Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma (Read the article)

  74. The bioinformatics of next generation sequencing: a meeting report (Read the article)

  75. Rapid detection of a mutation causing X-linked leucoencephalopathy by exome sequencing (Read the article)

  76. Comparison of Dengue Virus Type 2-Specific Small RNAs from RNA Interference-Competent and -Incompetent Mosquito Cells (Read the article)

  77. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery (Read the article)

  78. Mutations in CEP57 cause mosaic variegated aneuploidy syndrome (Read the article)

  79. Leber Congenital Amaurosis: Development Of A Comprehensive Molecular Genetic Test Panel Using Next-generation Sequencing (Read the article)

  80. Development of a service for hypertrophic cardiomyopathy using next generation sequencing - translation into a diagnostic laboratory, Oxford Molecular Genetics Laboratory,Oxford Biomedical Research Centre, Jessica Woodley & Sarah Reid (Read the article)

  81. Rapid detection of a mutation causing X-linked leucoencephalopathy by exome sequencing Conventional PCR-based direct sequencing of candidate genes for a family with X-linked leucoencephalopathy with unknown aetiology failed to identify any causative mutations. (Read the article)

  82. Pennsylvania State University Annual Progress Report: 2009 Formula Grant Reporting Period January 1, 2010 - June 30, 2010 (Read the article)

  83. Development and implementation of diagnostic services using NGS NextGENe (SoftGenetics) software - conversion to appropriate format. (Read the article)

  84. Next Generation Sequencing of BRCA1 and BRCA2: One Year On Data analysis using NextGENe (SoftGenetics) software. (Read the article)

  85. Next-gen sequencing in clinical debuts College of American Pathologists, April 2011
    Feature Story (Read the article)

  86. Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense. Ann M Hess, Abhishek N Prasad, Andrey Ptitsyn, Gregory D Ebel, Ken E Olson, Catalin Barbacioru, Cinna Monighetti and Corey L Campbell. (Read the article)

  87. Comparison of Dengue Virus Type 2-Specific Small RNAs from RNA Interference-Competent and -Incompetent Mosquito Cells. Jaclyn C. Scott, Doug E. Brackney, Corey L. Campbell, Virginie Bondu-Hawkins, Brian Hjelle, Greg D. Ebel, Ken E. Olson, Carol D. Blair. (Read the article)

  88. Genome-wide Studies of Copy Number Variation and Exome Sequencing Identify Rare Variants in BAG3 as a Cause of Dilated Cardiomyopathy. N Norton, D Li, MJ Rieder, JD Siegfried… - The American Journal of …, 2011. Sequence alignment to human reference sequences and expression quantification in RPKM were performed with the NextGENe software package (SoftGenetics, State College, PA) (Read the article)

  89. Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata
    (Lepidoptera: Crambidae)
    (Read the article)

  90. The utility of next-generation sequencing in the evaluation of the posterior polymorphous corneal dystrophy 1 locus. The utility of next-generation sequencing in the evaluation of the posterior polymorphous corneal dystrophy 1 locus. http://www.ncbi.nlm.nih.gov/pubmed/21203404

  91. High resolution, next generation sequencing from formalin fixed paraffin embedded archival material. P Chambers1, J Morgan1, K Southward2, P Quirke2, GR Taylor1. 1:Translational Genomics, Leeds institute of Molecular Medicine; 2:Pathology and Tumour Biology, Leeds Institute of Molecular Medicine, Leeds University. Current generation DNA sequencers have limited sequencing capacity and whilst formalin fixed paraffin embedded tissue can be sequenced, conventional methods are not quantitative. Next generation DNA sequencing allows the generation of 2.3 Gbases of sequence data per week or can be used to look at single lengths of DNA at extremely high resolution but have not yet beed applied to archival material. We have investigated whether next generation sequencing is possible using such material and what resolution is achievable. DNA was extracted from formalin fixed paraffin embedded tissue samples of colorectal cancer using proteinase K and a phenol:choloroform extraction. An 80bp amplimer encoding KRAS codons 12 and 13 and an 86bp amplimer encoding KRAS codon 61 were amplified and prepared for sequencing. The amplimers were ligated to each other, circularised and large molecular weight DNA generated by rolling circle amplification with phi29 polymerase. This DNA was randomly fragmented, end repaired and had adapters ligated prior to next generation sequencing. It was run on an Illumina GAII next generation analyser. The DNA sequence derived from the sequencer was analysed by NextGENe Software. It was found possible to generate sequence data on 700,000 individual sequences present within the cancer. Noise was minimal. Such technology will allow the deep sequencing of tumours from paraffin embedded tumour tissues to look for the evolution of small clones and quantitate their relative size as well as opening up the possibility of large scale multiplexing of samples on such machines.

  92. Gordana Raca, Craig Jackson, Berta Warman, Tom Bair, Lisa A. Schimmenti. Next generation sequencing in research and diagnostics of ocular birth defects. Molecular Genetics and Metabolism. March 2010. (Read the article)

  93. Genetic diagnosis of familial breast cancer using clonal sequencing J. Morgan, et al, Human Mutation, 2 Feb 2010
    (Link: http://www3.interscience.wiley.com/journal/123271389/abstract?CRETRY=1&SRETRY=0)

  94. Next-generation sequencing technologies and their implications for crop genetics and breeding R. Varshney et al Trends in Biotechnology Volume 27, Issue 9, September 2009, Pages 522-530
    (Read the article)

  95. The Handbook of Plant Mutation Screening: Mining of Natural and Induced Alleles
    edited by Khalid Meksem, Guenter Kahl Wiley-VCH.
    (Link: http://www.wiley.com/WileyCDA/WileyTitle/productCd-3527326049.html)

  96. Genome-wide dissection of globally emergent multi-drug resistant serotype 19A Streptococcus pneumonia D. Pillai, et al, BMC Genomics 2009, 10:642doi:10.1186/1471-2164-10-642

  97. DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data, S. Duncan et al, BMC Bioinformatics vol. 11
    (Link: http://www.biomedcentral.com/1471-2105/11/100)

  98. Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system, Sha Tang and Taoshen Huang BioTechniques, Vol. 48, No. 4, April 2010
    (Link: http://www.biotechniques.com/BiotechniquesJournal/2010/April/Characterization-of-mitochondrial-DNA-heteroplasmy-using-a-parallel-sequencing-system/biotechniques-197512.html?service=print)

  99. Meredith Yeager, Zuoming Deng , Joseph Boland, Casey Matthews, Jennifer Bacior, Victor Lonsberry, Amy Hutchinson, Laura A. Burdett, Liqun Qi, Kevin B. Jacobs, Jesus Gonzalez-Bosquet, Sonja I. Berndt, Richard B. Hayes, Robert N. Hoover, Gilles Thomas, David J. Hunter, Michael Dean and Stephen J. Chanock. Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.  Human Genetics: 2009, December, v.126: 743-750. Read the entire paper...click here.
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  100. Hemang Parikh, Zuoming Deng, Meredith Yeager, Joseph Boland, Casey Matthews, Jinping Jia, Irene Collins, Ariel White, Laura Burdett, Amy Hutchinson, Liqun Qi, Jennifer A. Bacior, Victor Lonsberry, Matthew J. Rodesch, Jeffrey A. Jeddeloh, Thomas J. Albert, Heather A. Halvensleben, Timothy T. Harkins, Jiyoung Ahn, Sonja I. Berndt, Nilanjan Chatterjee, Robert Hoover, Gilles Thomas, David J. Hunter, Richard B. Hayes, Stephen J. Chanock and Laufey Amundadottir. *A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33*. Human Genetics, 2010, January. 127:1. 91-99. Read the entire paper...click here.
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  101. Lan-Szu Chou,C.-S. Jonathan Liu, Benjamin Boese, Xinmin Zhang, Rong Mao. DNA Sequence Capture and Enrichment by Microarray Followed by Next-Generation Sequencing for Targeted Resequencing: Neurofibromatosis Type 1 Gene as a Model. Clinical Chemistry, 2010, January, 56:1, 62-72. Read the entire paper...click here.

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