Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

Niranjan, Tejasvi; Adamczyk, Abby; Bravo, Héctor Corrada; Taub, Margaret A.; Wheelan, Sarah J.; Irizarry, Rafael A.; Wang, Tao

doi:10.1186/gb-2011-12-9-r93

Cited by 9 publications

(12 citation statements)

References 19 publications

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“…We have previously observed that many false positive variant calls can be efficiently and specifically removed by applying two pre-filters determined by the proportion of base call from opposing strands and by inter-variant proximity [ 22 ]. Firstly, during read alignment, sequenced reads may be aligned to either the positive (Crick) or negative (Watson) strand.…”

Section: Resultsmentioning

confidence: 99%

“…A large portion of the variants in dbSNP that have a MAF > 0.73% are re-discovered and removed given the sample size of our study, thus explaining why our filter outperforms the “Non-Clinical” dbSNP filter. Additionally, we have previously observed that false positive variant calls occur in parallel in multiple samples due to systematic errors in preparation or sequencing of the same library [ 22 ]. As an added advantage, our strategy removes these variants by comparing samples prepared in the same library, a process of self-neutralizing these reoccurring systematic errors.…”

Section: Resultsmentioning

confidence: 99%

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Affected Kindred Analysis of Human X Chromosome Exomes to Identify Novel X-Linked Intellectual Disability Genes

et al. 2015

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X-linked Intellectual Disability (XLID) is a group of genetically heterogeneous disorders caused by mutations in genes on the X chromosome. Deleterious mutations in ~10% of X chromosome genes are implicated in causing XLID disorders in ~50% of known and suspected XLID families. The remaining XLID genes are expected to be rare and even private to individual families. To systematically identify these XLID genes, we sequenced the X chromosome exome (X-exome) in 56 well-established XLID families (a single affected male from 30 families and two affected males from 26 families) using an Agilent SureSelect X-exome kit and the Illumina HiSeq 2000 platform. To enrich for disease-causing mutations, we first utilized variant filters based on dbSNP, the male-restricted portions of the 1000 Genomes Project, or the Exome Variant Server datasets. However, these databases present limitations as automatic filters for enrichment of XLID genes. We therefore developed and optimized a strategy that uses a cohort of affected male kindred pairs and an additional small cohort of affected unrelated males to enrich for potentially pathological variants and to remove neutral variants. This strategy, which we refer to as Affected Kindred/Cross-Cohort Analysis, achieves a substantial enrichment for potentially pathological variants in known XLID genes compared to variant filters from public reference databases, and it has identified novel XLID candidate genes. We conclude that Affected Kindred/Cross-Cohort Analysis can effectively enrich for disease-causing genes in rare, Mendelian disorders, and that public reference databases can be used effectively, but cautiously, as automatic filters for X-linked disorders.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Affected Kindred Analysis of Human X Chromosome Exomes to Identify Novel X-Linked Intellectual Disability Genes

et al. 2015

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“…We used next-generation technology to sequence all 120 protein coding exons (including alternative exons) of NRG1 and NRG3 , the NRG receptor gene ERBB4 , the BACE1 gene, which encodes β-secretase enzyme, and the six genes that encode the components of the γ-secretase multiprotein complex ( PSEN1 , PSEN2 , PSENEN , NCSTN , APH1A and APH1B ), totaling 38.9 kb of genomic sequence. We sequenced amplified DNA from pools of four subjects (12 pools in total) following the procedures reported by Niranjan et al 50 with minor modifications. We aligned the reads to the reference human genome sequence (hg19 build) using the Bowtie alignment program, 51 and subsequently processed, sorted and indexed using SAMtools.…”

Section: Methodsmentioning

confidence: 99%

Multiple variants aggregate in the neuregulin signaling pathway in a subset of schizophrenia patients

et al. 2013

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Despite the strongly held view that schizophrenia (SZ) shows substantial genetic heterogeneity, pathway heterogeneity, as seen in cancer where different pathways are affected in similar tumors, has not been explored. We explore this possibility in a case-only study of the neuregulin signaling pathway (NSP), which has been prominently implicated in SZ and for which there is detailed knowledge on the ligand- and receptor-processing steps through β- and γ-secretase cleavage. We hypothesize that more than one damaging variants in the NSP genes might be necessary to cause disease, leading to an apparent clustering of such variants in only the few patients with affected NSP. We analyze linkage and next-generation sequencing results for the genes encoding components of the pathway, including NRG1, NRG3, ERBB4, β-secretase and the γ-secretase complex. We find multiple independent examples of supporting evidence for this hypothesis: (i) increased linkage scores over NSP genes, (ii) multiple positive interlocus correlations of linkage scores across families suggesting each family is linked to either many or none of the genes, (iii) aggregation of predicted damaging variants in a subset of individuals and (iv) significant phenotypic differences of the subset of patients carrying such variants. Collectively, our data strongly support the hypothesis that the NSP is affected by multiple damaging variants in a subset of phenotypically distinct patients. On the basis of this, we propose a general model of pathway heterogeneity in SZ, which, in part, may explain its phenotypic variability and genetic complexity.

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“…We identified multiple missense mutations clustered at PDZ4-6 of GRIP1 in a cohort of patients with autism [28,29]. These autism-associated mutations showed a gain-of-function effect manifesting an increase in binding with GluA2 in yeast-two-hybrid assay and an accelerated recycling of GluA2 in hippocampal neurons [28].…”

Section: Introductionmentioning

confidence: 99%

Mice lacking GRIP1/2 show increased social interactions and enhanced phosphorylation at GluA2-S880

Han

Mejı́as

Chiu

et al. 2017

Behavioural Brain Research

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Glutamate receptor interacting proteins 1 and 2 (GRIP1/2) play an important role in regulating synaptic trafficking of AMPA receptor 2/3 (GluA2/3) and synaptic strength. Gain-of-function GRIP1 mutations are implicated in social behavioral deficits in autism. To study mechanisms of Grip1/2-mediated AMPA signaling in the regulation of social behaviors, we performed social behavioral testing on neuron-specific Grip1/2-double knockout (DKO) and wild type (WT) mice that are matched for age, sex, and strain background. We determined the expression profile of key signaling proteins in AMPAR, mGluR, mTOR, and GABA pathways in frontal cortex, striatum, and cerebellum of DKO mice. Compared to WT mice, DKO mice show increased sociability in a modified three-chamber social behavioral test [mean ± sem for interaction time in seconds; WT: 44.0 ± 5.0; n = 10; DKO: 81.0 ± 9.0; n = 9; two factor repeated measures ANOVA: F(1,37) = 14.45; p < 0.01 and planned t-test; p < 0.01] and in a dyadic male–male social interaction test (mean ± sem for total time in seconds: sniffing, WT-WT, 18.9 ± 1.1; WT-DKO, 42.5 ± 2.1; t-test: p < 0.001; following, WT-WT, 7.7 ± 0.72; WT-DKO,14.4 ± 1.8; t-test: p < 0.001). Immunoblot studies identified an increase in phosphorylation at GluA2-Serine 880 (GluA2-pS880) in frontal cortex (mean ± sem; WT: 0.69 ± 0.06, n = 5; DKO: 0.96 ± 0.06, n = 6; t-test; p < 0.05) and reduced GABAβ3 expression in striatum (mean ± sem; WT: 1.16 ± 0.04, n = 4; DKO: 0.95 ± 0.06, n = 4; t-test; p < 0.05) in DKO mice. GluA2-S880 phosphorylation is known to regulate GluA2synaptic recycling, AMPA signaling strength and plasticity. GABAβ3 has been implicated in the etiology and pathogenesis in autism. These data support an important role of Grip1/2-mediated AMPA signaling in regulating social behaviors and disturbance of glutamate-and GABA-signaling in specialized brain regions in autism-related social behavioral deficits.

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Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

Cited by 9 publications

References 19 publications

Affected Kindred Analysis of Human X Chromosome Exomes to Identify Novel X-Linked Intellectual Disability Genes

Affected Kindred Analysis of Human X Chromosome Exomes to Identify Novel X-Linked Intellectual Disability Genes

Multiple variants aggregate in the neuregulin signaling pathway in a subset of schizophrenia patients

Mice lacking GRIP1/2 show increased social interactions and enhanced phosphorylation at GluA2-S880

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