Direct validation of imputed non-synonymous SNP alleles.
Glendon J. Parker
Tami Leppert
Deon S. Anex
Jonathan K. Hilmer
Nori Matsunami
Lisa Baird
Jeffery Stevens
Krishna Parsawar
Blythe P. Durbin-Johnson
David M. Rocke
Chad Nelson
Daniel J. Fairbanks
Andrew S. Wilson
Robert H. Rice
Scott R. Woodward
Brian Bothner
Bradley R. Hart
Mark Leppert
10.1371/journal.pone.0160653.g001
https://plos.figshare.com/articles/figure/Direct_validation_of_imputed_non-synonymous_SNP_alleles_/3812199
<p><b>A</b>) Genetically variant peptides (GVPs) that contained single amino-acid polymorphisms (SAPs) were identified in both European-American cohorts (EA1 and EA2) and collated for each subject. Imputed nsSNP alleles (Gene Name = GN, SNP accession number = rs#, allele nucleotide = nuc) were directly compared to the genotype resulting from direct Sanger sequencing (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160653#pone.0160653.s011" target="_blank">S1 Methods</a>). Correctly imputed nsSNP alleles (TP, true positives) are indicated by a blue square. Imputed alleles that were incorrectly predicted (FP, false positive) are indicated by red squares. Alleles that were identified using Sanger sequencing, but did not contain a resulting GVP in the matching proteomic dataset (FN, false negative) are indicated by light green squares. Alleles absent in both subjects DNA and in resulting proteomic datasets (TN, true negatives) are indicated by white squares[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160653#pone.0160653.ref049" target="_blank">49</a>]. Failed Sanger sequencing determination of nsSNP allelic status is indicated by grey. <b>B</b>) The effectiveness of each SAP-containing peptide to impute nsSNP alleles was also quantified. The sensitivity of each genetically variant peptide, measured as the proportion of nsSNP-alleles that are correctly detected and imputed (TP/(TP+FN)), was calculated as a percentage (log<sub>10</sub>(%). The positive predictive value (PPV) of genetically variant peptide-based SNP imputations was calculated as the percentage of correct validated SNP imputations of all imputations (TP/(TP + FP); log<sub>10</sub>(%))[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160653#pone.0160653.ref049" target="_blank">49</a>]. <b>C</b>)</p>
2016-09-07 17:30:01
Hair Shaft Proteome Human identification
African population
non-synonymou
hair shaft datasets
PCR
Genetically variant peptides
66 European-American subjects
mass spectrometry-based shotgun proteomics
nucleotide polymorphism profiles
hair shaft proteins
DNA
Protein-Based Human Identification
nucleotide polymorphism allelic profiles
nucleotide polymorphism alleles
hair shaft protein