Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine

Ellen Tsai,Matthew Lebo,Rimma Shakbatyan,Himanshu Sharma,Chiao-Feng Lin,Chet Graham,Peter Rossetti,Jason Evans

doi:10.3390/jpm6010012

Abstract

Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient’s genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS.

Highlights

Precision medicine is becoming an increasing focus in medical research [1]
Of 425 total confirmed variants, all 425 variants were detected by genome sequencing for a sensitivity of 100%
Four likely reference sequence errors, positions where only the alternative allele has ever been identified, were correctly genotyped by genome sequencing as homozygous for the alternative allele, three of which had incorrect genotype calls with previous orthogonal assays. In addition to these true positive variants, calls were made for 21 false positive (FP) variants, including 20 substitutions and one indel (Table 1b)

Summary

Introduction

Precision medicine is becoming an increasing focus in medical research [1]. To achieve the resolution necessary to personalize clinical care, greater attention has been drawn towards higher resolution of the patient genome. Generation sequencing (NGS) provided a cost-effective method for targeted sequencing of known disease genes at base pair resolution [2]. The advent of exome sequencing enabled rapid discovery of genes causing Mendelian disorders. While gene panels and exome sequencing have proved fast and cost-effective for delivering genomic results back to the patient, these technologies are limited by our current knowledge of the exome, which changes over time. The use of targeted capture may introduce biases to the data, including PCR duplicates, depth of coverage disparities, and failures at difficult to amplify target regions [3]

Methods

Results

Discussion

Conclusion