Sequencing

11th Annual Sequencing, Finishing, and Analysis in the Future Meeting
THE EXOME COVERAGE AND IDENTIFICATION
(EXCID) REPORT: A GENE SURVEY TOOL FOR
CLINICAL SEQUENCING APPLICATIONS
Wednesday, 1st June 20:00 La Fonda Mezzanine (2nd Floor) Poster (PS‐2b.10)
Rashesh Sanghvi, Kimberly Walker, Qiaoyan Wang, Harsha Doddapaneni, Yi Han,
Huyen Dinh, Eric Boerwinkle, Donna Muzny, Richard Gibbs
Baylor College of Medicine
The Exome Coverage and Identification (ExCID) Report was developed at the Baylor College of
Medicine Human Genome Sequencing Center (BCM‐HGSC) to represent gene, transcript and exon
sequence coverage for samples analyzed with panel sequencing, WES and WGS. Since March 2013,
the report has been used to analyze more than 22,888 WES, 9,428 regional captures and 32,660 WGS
research samples for the BCM‐HGSC and more than 23,647 WES/Carrier/CAP‐CLIA samples at Baylor
Miraca Genetics Laboratories (BMGL).
ExCID is a one‐stop tool for providing annotations, gathering mapping metrics such as %reads mapped
and %duplicates reads, coverage metrics such as average coverage and bases 20X, gene% coverages
for OMIM genes and reporting exact bases that are poorly covered based on user‐defined coverage
threshold. ExCID provides gene, transcript and exon annotations to the input BED regions from
RefSeq, VEGA, CCDS and MIRbase. These external databases are downloaded with the installation
of ExCID and can be updated using the scripts provided in the installation.
The user can visualize coverage over the region of interest using the UCSC tracks (WGS and BigBed)
and the OMIM Gene % coverages bar chart. Results are reported as boxplots and other ‘coverage
tracks’ that can be visualized in popular browsers such as the Integrative Genome Viewer (IGV)
and the UCSC Genome Browser. ExCID output was utilized by BMGL website to provide clinicians
easy access to in‐depth information on clinical design aspects and coverage.
In addition, ExCID’s batch ability makes it possible to compare data from hundreds of samples to
reveal trends in the performance of large scale sequencing projects and asses the consistency of
sequencing strategies. This can be used to determine the common problematic regions across
samples leading to design improvements and unique solutions. Analyzing clinical WES samples led
to technical developments such as capture reagent spike‐in (i.e. panel killer) and improving coverage
of nearly all clinically targeted genes (N=3,200 at 100% coverage). Furthermore, ExCID is used for
evaluating the efficiency of in‐house pipelines to meet requirements and set thresholds for various
coverage metrics. ExCID’s ability to asses the percentage of gene covered is routinely used both
clinical and research setting to samples with irregular performance. ExCID has also been used by
the Clinical Sequencing Exploratory Research (CSER) Sequencing Standards working group, a
consortium of ten clinical sequencing centers across the country, to determine the regions of the
genome that remain difficult to sequence, regardless of the method used. Establishment of robust
WGS pipeline metrics are essential for broad applications in both the research and clinical setting.
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