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Monday, August 8, 2016

Publication roundup: HGMD

Scientists often turn to HGMD, the Human Gene Mutation Database, as their first stop for learning about reported genetic mutations. Recent publications citing HGMD have used it for analyzing variants in patients with breast cancer and skeletal dysplasia, developing a carrier screening test, evaluating variants classified as pathogenic in epilepsy, and more.

Whole-exome sequencing reveals a novel COL2A1 mutation in a patient with spondyloepiphyseal dysplasia congenita
First author: A. Sangsin

In this Genetics and Molecular Research paper, scientists in Thailand used whole-exome sequencing to diagnose an infant with skeletal dysplasia. Using HGMD to filter out known pathogenic mutations, they identified a de novo non-synonymous variant that allowed them to provide a more specific diagnosis for the patient.

Population-based preconception carrier screening: how potential users from the general population view a test for 50 serious diseases
First author: Mirjam Plantinga

In a project spanning institutes in the Netherlands and the UK, scientists developed a preconception carrier screening test for couples that reveals the likelihood of passing on any of 50 serious, untreatable autosomal recessive diseases. In this European Journal of Human Genetics paper, they report the results of a survey collecting information about how prospective parents respond to this kind of test. For the screening test, they assessed variants with HGMD.

Comparative analysis of BRCA1 and BRCA2 variants of uncertain significance in patients with breast cancer: a multifactorial probability-based model versus ACMG standards and guidelines for interpreting sequence variants
First author: Kyung Sun Park

Scientists in Korea used HGMD and other data repositories to analyze variants of unknown significance in the BRCA1 and BRCA2 genes, reporting the results of their work in this Genetics in Medicine paper. By studying more than 700 Korean breast cancer patients, they investigated more than 40 variants of unknown significance and came to the conclusion that genetic counseling should be based on concordant results.

Evaluation of Presumably Disease Causing SCN1A Variants in a Cohort of Common Epilepsy Syndromes
First author: Dennis Lal

Scientists in Europe and the US assessed previously classified variants in an epilepsy risk gene to determine whether benign variants had been misreported as pathogenic; in this PLoS One paper, they detail their findings. They used the HGMD Professional version for variant annotation, and also validated all SCN1A variants listed in HGMD with Sanger sequencing.

Mining clinical attributes of genomic variants through assisted literature curation in Egas
First author: Srgio Matos

Scientists in Portugal and the UK published this article in the Database journal, reporting the use of a web-based text-mining solution to curate clinical attributes in the literature. They used the comprehensive HGMD collection to train their curation algorithm, and then used it to annotate 100 Medline abstracts as a proof of principle.

Clinical and Molecular Characterization of NF1 Patients: Single-Center Experience of 32 Patients From China
First authors: Lude Zhu and Yunfeng Zhang

Scientists in China developed a streamlined protocol for detecting neurofibromatosis type 1 mutations from blood. NF1 detection is challenging due to its large size, number of mutations, pseudogenes, and more. The team cites more than 1,000 NF1 mutations that are reported in HGMD, and they contributed new data on these variants back to the database.

Learn more about HGMD