Nomenclature for the description of human sequence variations

Dunnen, Johan T. den; Antonarakis, Stylianos E.

doi:10.1007/s004390100505

Cited by 840 publications

(425 citation statements)

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“…This mutation was named 1262_1289delinsTGACTTTCAT, in agreement with the nomenclature for human sequence variations 29. Moreover, 2 new ITDs were found in exon 11 (Fig 2): a first one, consisting in the insertion of 12 AAs at the residue 571 (ITD 571–582 ); and a second one based on an addition of 14 AAs at the residue 574 (ITD 574–587 ).…”

Section: Resultssupporting

confidence: 70%

Concordance of c‐kit Mutational Status in Matched Primary and Metastatic Cutaneous Canine Mast Cell Tumors at Baseline

Marconato

Zorzan

Giantin

et al. 2013

Veterinary Internal Medicne

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BackgroundMutation analysis of proto‐oncogene c‐kit (c‐kit) is advisable before starting treatment with tyrosine kinase inhibitors in dogs with mast cell tumor (MCT), including those with metastatic disease. Testing is usually performed on primary tumors, assuming that c‐kit mutation status does not change in metastasis.Hypothesis/ObjectivesTo give an insight into the mutational processes and to make a recommendation on the use of c‐kit mutational analysis in the clinical setting.AnimalsTwenty‐one client‐owned dogs with metastatic MCT.MethodsDogs undergoing resection or biopsy for both primary and matched metastatic MCT were prospectively enrolled. Total RNA or DNA was extracted from primary MCT and corresponding metastases. Exons 8, 9, and 11 were amplified by PCR and sequenced. Genetic features between primary MCT and metastases were compared. Their correlation with clinicopathologic features was investigated.ResultsConcordance (mutated or wild‐type) of mutational status, evaluable in 21 primary and matched metastatic (20 nodal and 1 splenic) MCTs, was 100%. Three new c‐kit mutations were identified. No significant correlation was detected between c‐kit mutation and clinicopathologic features.Conclusions and Clinical ImportanceProto‐oncogene c‐kit mutational status is conserved between any primary and its matched secondary tumor, suggesting that both can be used for c‐kit mutational testing. Targeted therapies might be also used to treat metastatic disease.

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Section: Resultssupporting

confidence: 70%

Concordance of c‐kit Mutational Status in Matched Primary and Metastatic Cutaneous Canine Mast Cell Tumors at Baseline

Marconato

Zorzan

Giantin

et al. 2013

Veterinary Internal Medicne

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“…Reference sequences used in this study are MLH1: NM_000249.2, MSH2: NM_000251.2, MSH6: NM_000179.2, and PMS2: NM_000535.5, and the nomenclature used are as recommended by the Human Gene Mutation Database (HGMD) (Den Dunnen and Antonarakis 2001). …”

Section: Methodsmentioning

confidence: 99%

Lynch syndrome mutation spectrum in New South Wales, Australia, including 55 novel mutations

Sjursen

McPhillips²,

Scott

et al. 2016

Molec Gen & Gen Med

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BackgroundLynch syndrome, the most frequent hereditary colorectal cancer syndrome, is caused by defects in mismatch repair genes. Genetic testing is important in order to identify mutation carriers who can benefit from intensive surveillance programs. One of the challenges with genetic testing is the interpretation of pathogenicity of detected DNA variants. The aim of this study was to investigate all putative pathogenic variants tested for at the Division of Molecular Medicine, Pathology North, in Newcastle, Australia, to establish whether previous variant classification is in accordance with that recently performed in the InSiGHT collaboration.MethodsPrediction programs and available literature were used to classify new variants or variants without classification.ResultsWe identified 333 mutation positive families, in which 211 different putative pathogenic mismatch repair mutations were found. Most variants with an InSiGHT classification (141 out of 146) were in accordance with our classification. Five variants were discordant, of which one can definitively be reclassified according to the InSiGHT scheme as class 5. Sixty‐four variants had not been classified by InSiGHT, of whom 55 have not been previously reported.ConclusionIn conclusion, we found that our classifications were mostly in accordance with the InSiGHT scheme. In addition to already known MMR mutations, we have also presented 55 novel pathogenic or putative pathogenic mutations.

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“…E3675_301) is provided, based on nomenclature from the SNP500Cancer project (Packer et al, 2006). Single nucleotide polymorphism locations were determined using the guidelines of the Human Genome Variation Society (den Dunnen and Antonarakis, 2001).…”

Section: Laboratory Methodsmentioning

confidence: 99%

Genetic variation in five genes important in telomere biology and risk for breast cancer

et al. 2007

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Telomeres, consisting of TTAGGG nucleotide repeats and a protein complex at chromosome ends, are critical for maintaining chromosomal stability. Genomic instability, following telomere crisis, may contribute to breast cancer pathogenesis. Many genes critical in telomere biology have limited nucleotide diversity, thus, single nucleotide polymorphisms (SNPs) in this pathway could contribute to breast cancer risk. In a population-based study of 1995 breast cancer cases and 2296 controls from Poland, 24 SNPs representing common variation in POT1, TEP1, TERF1, TERF2 and TERT were genotyped. We did not identify any significant associations between individual SNPs or haplotypes and breast cancer risk; however, data suggested that three correlated SNPs in TERT (À1381C4T, À244C4T, and Ex2-659G4A) may be associated with reduced risk of breast cancer among individuals with a family history of breast cancer (odds ratios 0.73, 0.66, and 0.57, 95% confidence intervals 0.53 -1.00, 0.46 -0.95 and 0.39 -0.84, respectively). In conclusion, our data do not support substantial overall associations between SNPs in telomere pathway genes and breast cancer risk. Intriguing associations with variants in TERT among women with a family history of breast cancer warrant follow-up in independent studies.

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Nomenclature for the description of human sequence variations

Cited by 840 publications

References 1 publication

Concordance of c‐kit Mutational Status in Matched Primary and Metastatic Cutaneous Canine Mast Cell Tumors at Baseline

Concordance of c‐kit Mutational Status in Matched Primary and Metastatic Cutaneous Canine Mast Cell Tumors at Baseline

Lynch syndrome mutation spectrum in New South Wales, Australia, including 55 novel mutations

Genetic variation in five genes important in telomere biology and risk for breast cancer

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