Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods.
As whole genome sequencing (WGS) uncovers variants associated with rare and common diseases, an immediate challenge is to minimize false-positive findings due to sequencing and variant calling errors. False positives can be reduced by combining results from orthogonal sequencing methods, but costly. Here, we present variant filtering approaches using logistic regression (LR) and ensemble genotyping to minimize false positives without sacrificing sensitivity. We evaluated the methods using paired WGS datasets of an extended family prepared using two sequencing platforms and a validated set of variants in NA12878. Using LR or ensemble genotyping based filtering, false-negative rates were significantly reduced by 1.1- to 17.8-fold at the same levels of false discovery rates (5.4% for heterozygous and 4.5% for homozygous single nucleotide variants (SNVs); 30.0% for heterozygous and 18.7% for homozygous insertions; 25.2% for heterozygous and 16.6% for homozygous deletions) compared to the filtering based on genotype quality scores. Moreover, ensemble genotyping excluded > 98% (105,080 of 107,167) of false positives while retaining > 95% (897 of 937) of true positives in de novo mutation (DNM) discovery in NA12878, and performed better than a consensus method using two sequencing platforms. Our proposed methods were effective in prioritizing phenotype-associated variants, and an ensemble genotyping would be essential to minimize false-positive DNM candidates.
Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Boston Children's Hospital, Boston, Massachusetts; School of Computer Science and Engineering, Soongsil University, Seoul, 156-743, South Korea.
Kyu-Baek
KB
Hwang
In-Hee
IH
Lee
Jin-Ho
JH
Park
Tina
T
Hambuch
Yongjoon
Y
Choe
MinHyeok
M
Kim
Kyungjoon
K
Lee
Taemin
T
Song
Matthew B
MB
Neu
Neha
N
Gupta
Isaac S
IS
Kohane
Robert C
RC
Green
Sek Won
SW
Kong
D000465:Algorithms; D045744:Cell Line, Tumor; D005189:False Positive Reactions; D015894:Genome, Human; D060005:Genotyping Techniques / Q000706:statistics & numerical data; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D006720:Homozygote; D006801:Humans; D033162:Incidental Findings; D016015:Logistic Models; D058977:Molecular Sequence Annotation; D016254:Mutagenesis, Insertional; D009154:Mutation; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*
ensemble genotyping; false positive; incidental finding; logistic regression; whole genome sequencing