Customizable
Reporting Options for Sanger Sequencing
Projects
Mutation Surveyor software offers
unique reporting options for Sanger
sequencing projects, including resequencing,
direct sequencing, PCR sequencing,
and mitochondrial DNA (mtDNA) sequencing
projects. Included in the software
is the versatile Custom Report,
which provides options to customize
everything from sample grouping
options to the types of mutations
displayed. Reporting and organization
options include the ability to reorganize
sample/patient files, hide specific
variants of non-interest, color-code
pathogenicity, organize and output
calls by specific regions of interest,
include trace quality information,
and report by preferred nomenclature
(genomic position, cDNA/CDS, mRNA,
HGVS, or custom nomenclature). Contained
in this report is a unique Normal
Allele Scoring method (NM_Score),
indicating the contribution of the
normal allele at the position compared
to the contribution of the possible
mutant alleles at the same position.
Following detection of single nucleotide
polymorphisms (SNPs), heterozygous
and homozygous insertions and deletions
(indels) and low-frequency variants
(somatic, heteroplasmic, mosaic),
the Custom Report template lets
the user build their own report
and quickly export in .txt, .xlsx,
.xml, and .vcf formats. A VCF file
allows for importation of results
into Geneticist
Assistant NGS Interpretative Workbench
enabling the generation of a historical
knowledge base of variants and annotation.
These reporting options in the Custom
Report provide enhanced flexibility
superior to anything found in similar
programs such as Applied Biosystems
SeqScape®, Variant Reporter®, and
Minor Variant Finder; DNAStar's
SeqMan Pro™; Gene Code's Sequencher®;
or JSI Medical Systems' SEQUENCE
PILOT, allowing users to quickly
meet internal reporting, LIMS, or
other database requirements.
Multiple
Sample Grouping Options

Figure
1: The Custom Report of
Mutation Surveyor allows users to
rapidly group sample files based
on up to three orders of grouping
options. Traces are initially grouped
on their 1st order grouping option,
and further sorting is carried out
based on 2nd and 3rd order grouping
options. Examples of grouping options
include sample or patient identifier,
contig, gene, exon, and trace position.
Mutation
Filtering

Figure
2: With a simple click
users can filter mutation calls
by parameters such as location within
the genome or mutation type. Users
can display mutations found within
all locations or target mutations
found in specific locations, such
as custom regions of interest, CDS,
or intronic mutations. A further
level of filtering can be applied
based on mutation type, which enables
users to filter based on criteria
such as silent, missense, nonsense,
indel, homozygous, heterozygous,
etc.
Trace Quality
Information

Figure
3: Quality metrics can
be used in the Custom Report to
identify traces and nucleotides
with low quality. Trace quality
can be assigned to the entire trace,
comparison region, or ROI/CDS and
can be reported relative to Phred
Score or Signal-to-Noise Ratio.
Those traces that do not meet a
specified quality threshold are
identified with a background color
that is selected by the user. Nucleotide
quality information can also be
used to identify specific nucleotides
that fall below thresholds set by
the user.
Identify
Variants with Color Codes

The
color-coding options of the Custom
Report provide a variety of options
to assist the user with identifying
different types of variants and
potential analysis problems. Both
text color coding and background
color coding can be applied to identify
areas of low quality, low confidence,
confirmed variants, and mutation
call discrepancies. Users can easily
switch between reports and the Graphical
Analysis Display for quick review
and confirmation by double-clicking
the specific variation in the mutation
table.

Normal Allele
Scoring
Mutation Surveyor
software provides a confidence check
on the absence of mutations at each
nucleotide, greatly assisting in
validating analysis results. All
scores can be shown in the report
by selecting the appropriate options.
|
Phred Score: 50
NM_Score: 20.5
High Score
Normal Allele
|
Phred Score: 20
NM_Score: 1.4
Moderate Score
Heterozygous
Substitution
|
Phred Score: 51
NM_Score: 0.0
Low Score
Homozygous
Substitution
|
Phred Score: 11
NM_Score: 5.2
High Score
False
Positive
|
Webinar
Custom Report Options
for Mutation Surveyor (View
on )
Trademarks property of their respective owner
|
|