Sentence examples for based on array genotypes from inspiring English sources

Genotype concordance (GC), non-reference sensitivity (NRS), non-reference genotype concordance (NRC), and precision were calculated based on array genotypes and corresponding sequence-based genotypes obtained with different variant callers (GATK [ 16], freebayes [ 30], SAMtools [ 15]).

(XLSX 13 kb) Additional file 6: Boxplot of genotype concordance, non-reference sensitivity, non-reference genotype concordance and precision calculated based on array genotypes and corresponding sequence-based genotypes obtained with different variant callers (GATK, freebayes, SAMtools) at positions where SNPs from the array were available on chromosomes 3, 6 and 28 (~50 k).

Another 839 (11.5%) appeared homozygous based on sequencing, and were heterozygous based on array genotyping, possibly due to absence of allele representation of alternate allele in sequence or presence of signal from paralogous sequences; and 40 (0.5%) had alternative homozygous genotypes.

The frequency of the associated haplotype was estimated to be 1.86% based on array-derived genotypes (see above).

In this context, SNPs identified by means of high-throughput genotyping based on array technology could be a useful tool [ 23, 24].

For obtaining dense and accurate next-generation RH maps, new methods were developed recently exploiting the increased availability of comparative genomic resources [ 12] and have proved successful for the production of RH maps based on SNP array genotyping data [ 13, 14].

These plots suggest that false positive findings are caused by imputation based on arrays of inferior quality, when cases and controls are not matched for genotyping platforms.

The conclusions of genetic research based on genotyping arrays can be influenced by SNP selection (ascertainment) bias.

When performing association based on genotyping arrays, it is common practice to impute untyped variants based on a reference panel (e.g. the 1000 Genomes Project (www.1000genomes.org) and/or the UK10K study data (www.uk10k.org) to enhance the resolution of the study.

Hou et al. [ 5] on the other hand, reported 682 CNVRs encompassing 370 loss, 216 gain and 96 loss and gain events in the same region in 521 animals representing 21 different breeds, also based on SNP genotyping arrays.

This is the mean of 666 pairwise correlations calculated based on 37 Linear Array genotyping test results collected in the 2003 2006 National Health and Nutrition Examination Survey NHANESS).