Category Archives: Hum Mutat

Assessment of variant pathogenicity in a highly admixed population.

Assessment of variant pathogenicity in a highly admixed population.
Hum Mutat. 2017 Jul;38(7):749
Authors: Guryev V
PMID: 28609575 [PubMed – in process]

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Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts.

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Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts.
Hum Mutat. 2015 Jul 29;
Authors: Lancaster O, Beck T, Atlan D, Swertz M, V… Continue reading

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High frequency of RPL22 mutations in microsatellite-unstable colorectal and endometrial tumors.

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High frequency of RPL22 mutations in microsatellite-unstable colorectal and endometrial tumors.
Hum Mutat. 2014 Dec;35(12):1442-5
Authors: Ferreira AM, Tuominen I, van Dijk-Bos K, Sanjabi B, van der … Continue reading

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New target genes in endometrial tumors show a role for the estrogen-receptor pathway in microsatellite-unstable cancers.

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New target genes in endometrial tumors show a role for the estrogen-receptor pathway in microsatellite-unstable cancers.
Hum Mutat. 2014 Dec;35(12):1514-23
Authors: Ferreira AM, Tuominen I, Sousa S, … Continue reading

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Evaluation of CADD scores in curated mismatch repair gene variants yields a model for clinical validation and prioritization.

Evaluation of CADD scores in curated mismatch repair gene variants yields a model for clinical validation and prioritization.

Hum Mutat. 2015 Apr 13;

Authors: van der Velde KJ, Kuiper J, Thompson BA, Plazzer JP, van Valkenhoef G, de Haan M, Jongbloed JD, Wijmenga C, de Koning TJ, Abbott KM, Sinke R, Spurdle AB, Macrae F, Genuardi M, Sijmons RH, Swertz MA, InSiGHT Group

Abstract
Next generation sequencing in clinical diagnostics is providing valuable genomic variant data, which can be used to support healthcare decisions. In silico tools to predict pathogenicity are crucial to assess such variants and we have evaluated a new tool, Combined Annotation Dependent Depletion (CADD), and its classification of gene variants in Lynch syndrome by using a set of 2210 DNA mismatch repair gene variants. These had already been classified by experts from InSiGHT’s Variant Interpretation Committee. Overall, we found CADD scores do predict pathogenicity (Spearman’s ρ = 0.595, p ≪ 0.001). However, we discovered 31 major discrepancies between the InSiGHT classification and the CADD scores; these were explained in favor of the expert classification using population allele frequencies, co-segregation analyses, disease association studies, or a second-tier test. Of 751 variants that could not be clinically classified by InSiGHT, CADD indicated that 47 variants were worth further study to confirm their putative pathogenicity. We demonstrate CADD is valuable in prioritizing variants in clinically relevant genes for further assessment by expert classification teams. This article is protected by copyright. All rights reserved.

PMID: 25871441 [PubMed – as supplied by publisher]

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The ARVD/C Genetic Variants Database: 2014 Update.

The ARVD/C Genetic Variants Database: 2014 Update.
Hum Mutat. 2015 Feb 10;
Authors: Lazzarini E, Jongbloed JD, Pilichou K, Thiene G, Basso C, Bikker H, Charbon B, Swertz M, van Tintelen JP, van der Zwaag PA
A… Continue reading

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An overview and online registry of microvillus inclusion disease patients and their MYO5B mutations.

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An overview and online registry of microvillus inclusion disease patients and their MYO5B mutations.
Hum Mutat. 2013 Dec;34(12):1597-605
Authors: van der Velde KJ, Dhekne HS, Swertz MA, Sirigu S, Rop… Continue reading

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A new coding system for metabolic disorders demonstrates gaps in the international disease classifications ICD-10 and SNOMED-CT, which can be barriers to genotype-phenotype data sharing.

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A new coding system for metabolic disorders demonstrates gaps in the international disease classifications ICD-10 and SNOMED-CT, which can be barriers to genotype-phenotype…

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Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics.

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Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics.

Hum Mutat. 2013 Jul;34(7):1035-42

Authors: Sikkema-Raddatz B,…

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Mutation update on the CHD7 gene involved in CHARGE syndrome.

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Mutation update on the CHD7 gene involved in CHARGE syndrome.

Hum Mutat. 2012 Aug;33(8):1149-60

Authors: Janssen N, Bergman JE, Swertz MA, Tranebjaerg L,…

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A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome.

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A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome.

Hum Mutat. 2012 Aug;33(8):1251-60

Authors: …

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Targeted exome sequencing in clear cell renal cell carcinoma tumors suggests aberrant chromatin regulation as a crucial step in ccRCC development.

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Targeted exome sequencing in clear cell renal cell carcinoma tumors suggests aberrant chromatin regulation as a crucial step in ccRCC development.

Hum Mutat. 2012…

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The use of arrays to detect copy-number variations in clinical practice.

The use of arrays to detect copy-number variations in clinical practice.

Hum Mutat. 2012 Jun;33(6):905

Authors: Sikkema-Raddatz B, Sijmons RH

PMID: 22570302 [PubMed – in…

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The international dystrophic epidermolysis bullosa patient registry: an online database of dystrophic epidermolysis bullosa patients and their COL7A1 mutations.

The international dystrophic epidermolysis bullosa patient registry: an online database of dystrophic epidermolysis bullosa patients and their COL7A1 mutations.

Hum Mutat. 2011…

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PROS1 analysis in 87 pedigrees with hereditary protein S deficiency demonstrates striking genotype-phenotype associations.

PROS1 analysis in 87 pedigrees with hereditary protein S deficiency demonstrates striking genotype-phenotype associations.
Hum Mutat. 2008 Jul;29(7):939-47
Authors: Ten Kate MK, Platteel M, Mulder R, Terpstra P, Nicolaes GA, R… Continue reading

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