Reply to Plüss et al.: The strength of PEMapper/PECaller lies in unbiased calling using large sample sizes

Johnston, H. Richard; Chopra, Pankaj; Wingo, Thomas S.; Patel, Viren; Epstein, Michael P.; Mullé, Jennifer G.; Warren, Stephen T.; Zwick, Michael E.; Cutler, David J.

doi:10.1073/pnas.1714535114

Cited by 1 publication

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References 5 publications

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“…36 In brief, samples were sequenced with the Illumina HiSeq X Ten for the first 100 samples and the Illumina HiSeq 2500 platform for all other samples at Hudson Alpha. Sequence reads were mapped to genome build hg38 (December 2013; GRCh38/ hg38) with PEMapper (90% stringency for 2 3 100 bp reads and 95% stringency for 2 3 150 bp reads; 37 ). Deletion sizes were confirmed by the coverage at the 22q11.2 region.…”

Section: Complete Sequencing Of the 22q112 Region And Quality-control Measuresmentioning

confidence: 99%

Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

Zhao¹,

Diacou²,

Johnston³

et al. 2020

The American Journal of Human Genetics

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The 22q11.2 deletion syndrome (22q11.2DS) results from non-allelic homologous recombination between low-copy repeats termed LCR22. About 60%-70% of individuals with the typical 3 megabase (Mb) deletion from LCR22A-D have congenital heart disease, mostly of the conotruncal type (CTD), whereas others have normal cardiac anatomy. In this study, we tested whether variants in the hemizygous LCR22A-D region are associated with risk for CTDs on the basis of the sequence of the 22q11.2 region from 1,053 22q11.2DS individuals. We found a significant association (FDR p < 0.05) of the CTD subset with 62 common variants in a single linkage disequilibrium (LD) block in a 350 kb interval harboring CRKL. A total of 45 of the 62 variants were associated with increased risk for CTDs (odds ratio [OR) ranges: 1.64-4.75). Associations of four variants were replicated in a meta-analysis of three genome-wide association studies of CTDs in affected individuals without 22q11.2DS. One of the replicated variants, rs178252, is located in an open chromatin region and resides in the double-elite enhancer, GH22J020947, that is predicted to regulate CRKL (CRK-like proto-oncogene, cytoplasmic adaptor) expression. Approximately 23% of patients with nested LCR22C-D deletions have CTDs, and inactivation of Crkl in mice causes CTDs, thus implicating this gene as a modifier. Rs178252 and rs6004160 are expression quantitative trait loci (eQTLs) of CRKL. Furthermore, set-based tests identified an enhancer that is predicted to target CRKL and is significantly associated with CTD risk (GH22J020946, sequence kernal association test (SKAT) p ¼ 7.21 3 10 À5 ) in the 22q11.2DS cohort. These findings suggest that variance in CTD penetrance in the 22q11.2DS population can be explained in part by variants affecting CRKL expression.

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Section: Complete Sequencing Of the 22q112 Region And Quality-control Measuresmentioning

confidence: 99%

Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

Zhao¹,

Diacou²,

Johnston³

et al. 2020

The American Journal of Human Genetics

Self Cite

View full text Add to dashboard Cite

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Reply to Plüss et al.: The strength of PEMapper/PECaller lies in unbiased calling using large sample sizes

Cited by 1 publication

References 5 publications

Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

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