Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes

Abstract

Purpose The contribution of common genetic variants to pre-cancer progression is understudied due to long follow-up time, rarity of poor outcomes and lack of available germline DNA collection. Alternatively, DNA from diagnostic archival tissue is available, but its somatic nature, limited quantity and suboptimal quality would require an accurate cost-effective genome-wide germline genotyping methodology. Experimental design Blood and tissue DNA from 10 individuals were used to benchmark the accuracy of Single Nucleotide Polymorphisms (SNP) genotypes, Polygenic Risk Scores (PRS) or HLA haplotypes using low-coverage whole-genome sequencing (lc-WGS) and genotype imputation. Tissue-derived PRS were further evaluated for 36 breast cancer patients (11.7 years median follow-up time) diagnosed with DCIS and used to model the risk of Breast Cancer Subsequent Events (BCSE). Results Tissue-derived germline DNA profiling resulted in accurate genotypes at common SNPs (blood correlation r2 > 0.94) and across 22 disease-related polygenic risk scores (PRS, mean correlation r = 0.93). Imputed Class I and II HLA haplotypes were 96.7% and 82.5% concordant with clinical-grade blood HLA haplotypes, respectively. In DCIS patients, tissue-derived PRS was significantly associated with BCSE (HR = 2, 95% CI 1.2–3.8). The top and bottom decile patients had an estimated 28% and 5% chance of BCSE at 10 years, respectively. Conclusions Archival tissue DNA germline profiling using lc-WGS and imputation, represents a cost and resource-effective alternative in the retrospective design of long-term disease genetic studies. Initial results in breast cancer suggest that common risk variants contribute to pre-cancer progression.

Polygenic Risk Score in Predicting Esophageal, Oropharyngeal, and Hypopharynx Cancer Risk among Taiwanese Population

“…Moreover, Tanigawa's PRS has played a role in several cohort studies with positive results. Nachmanson et al found that in patients with breast ductal carcinoma, the tissue-derived PRS was significantly associated with breast cancer subsequent events (HR = 2, 95% CI 1.2-3.8) [24]. Our study represents the first GWAS cohort to examine Tanigawa's PRS in patients with SCCs of the upper gastrointestinal tract.…”

Assessment of DNA quality for whole genome library preparation

“…While the use of microarrays has long been the state of the art for SNP genotyping, the requirement for high amounts of pure and intact DNA limits its application for several types of challenging samples [10,18]. The recent progress in sequencing techniques has enabled the analysis of low quantities of degraded DNA [19][20][21][22] and the successful generation of genotypes from aged samples [1, 10,14,[23][24][25][26][27]. The possibility of re-analyzing difficult DNA samples with more sophisticated methods has also spurred the continuation and reopening of unsolved investigations of "cold cases" and unidentified human remains [14,24,26].…”