Sequencing
SFAF2016%20Meeting%20Guide%20Final%203
SFAF2016%20Meeting%20Guide%20Final%203
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11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting<br />
EVALUATION OF HISEQ X TEN PERFORMANCE:<br />
TOWARDS CLINICAL APPLICATIONS<br />
Friday, 3rd June 16:20 La Fonda Ballroom Talk (OS‐10.02)<br />
Kimberly Walker 1 , Rashesh Sanghvi 1 , Qiaoyan Wang 1 , Harsha Doddapaneni 1 , Jianhong Hu 1 , Adam<br />
English 1 , William Salerno 1 , Yi Han 1 , Huyen Dinh 1 , Eric Boerwinkle 2 , Richard Gibbs 1 , Donna Muzny 1<br />
1 Human Genome <strong>Sequencing</strong> Center Baylor College of Medicine,<br />
2 University of Texas Health Science Center at Houston<br />
High‐throughput parallel nucleotide sequencing has revolutionized genomic research and reshaped<br />
applications in clinical health care. The HiSeq X Ten platform further expands these opportunities<br />
with unprecedented capacity. The Human Genome <strong>Sequencing</strong> Center (HGSC) at Baylor College of<br />
Medicine adopted the HiSeq X Ten system in the fall of 2014, with a view to eventual deployment<br />
in a CAP/CLIA environment.<br />
To evaluate the instruments, we have analyzed more than 1,093 flowcells, representing >8,441 30X<br />
human genomes. These studies have included common disease cohorts, inherited cancers, mendelian<br />
disease cases as well as DNA from cell lines of lung and endometrial cancer. PCR‐Free library methods<br />
(Illumina, Kapa Biosystems, and Swift Biosciences) have been evaluated and implemented for<br />
optimize coverage in GC‐rich regions. Metrics related to coverage, sample integrity and variant<br />
representation were established to ensure high quality genome sequencing.<br />
Based on our experience with the HiSeq X platform, we have implemented several standard metrics<br />
including >53% Pass Filter, >90% aligned bases, 85% unique reads and >75%<br />
Q30 bases to achieve at least 90 GB unique aligned bases per lane. These are utilized for daily<br />
tracking of quality. Genome coverage metrics are also tracked to achieve 90% of genome covered<br />
at 20x and 95% at 10x with a minimum of 86 x 109 mapped, aligned bases with Q20 or higher.<br />
Additional metrics such as library insert size (mode and mean) per sample, duplicate reads, read<br />
1 and read 2 error rates, % pair reads and mean quality scores are also monitored. Platform sensitivity<br />
and precision at ~30 coverage was determined to be 97.8% and 99.6% respectively using control<br />
sample NA12878. To ensure integrity in our production pipeline, we have implemented the<br />
SNPTrace assay by Fluidigm to confirm sample identity and VerifyBamID to detect sample<br />
contamination. Assessment of appropriate coverage benchmarks for clinically relevant genes and<br />
variants utilizing the OMIM gene list is in progress.<br />
These evaluation efforts have provided valuable insight as to how sequencing depth and coverage<br />
uniformity impact the ability to accurately detect variants. Overall the platform has been consistent<br />
in performance. Recent data has shown stability in platform run‐to‐run yield and quality in more<br />
than 1,600 PCR‐Free Kapa Hyper library samples achieving the high quality metrics described above.<br />
Establishment of robust PCR‐Free WGS methods and associated pipeline metrics are essential for<br />
broad applications in both the research and clinical setting.<br />
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