Genome Medicine

http://link.springer.com/journal/13073

List of Papers (Total 1,049)

Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease

BackgroundPulmonary arterial hypertension (PAH) is a rare disease characterized by distinctive changes in pulmonary arterioles that lead to progressive pulmonary arterial pressures, right-sided heart failure, and a high mortality rate. Up to 30% of adult and 75% of pediatric PAH cases are associated with congenital heart disease (PAH-CHD), and the underlying etiology is largely...

Red blood cell indices and anaemia as causative factors for cognitive function deficits and for Alzheimer’s disease

BackgroundStudies have shown that low haemoglobin and anaemia are associated with poor cognition, and anaemia is known to be associated with Alzheimer’s disease (AD), but the mechanism of this risk is unknown. Here, we first seek to confirm the association between cognition and anaemia and secondly, in order to further understand the mechanism of this association, to estimate the...

Genomic surveillance of avian-origin influenza A viruses causing human disease

Editorial summaryAvian influenza A viruses (AIVs) pose a threat to global health because of their sporadic zoonotic transmission and potential to cause pandemics. Genomic surveillance of AIVs has become a powerful, cost-effective approach for studying virus transmission, evolution, and dissemination, and has the potential to inform outbreak control efforts and policies.

A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing

Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used...

Getting up close and personal with UK genomics and beyond

Stephan Beck discusses recent developments in sharing personal genomes as part of the Personal Genome Project in the UK and globally, and how these efforts are advancing research.

Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes

Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using...

MutationalPatterns: comprehensive genome-wide analysis of mutational processes

BackgroundBase substitution catalogues represent historical records of mutational processes that have been active in a cell. Such processes can be distinguished by various characteristics, like mutation type, sequence context, transcriptional and replicative strand bias, genomic distribution and association with (epi)-genomic features.ResultsWe have created MutationalPatterns, an...

Enabling multiplexed testing of pooled donor cells through whole-genome sequencing

We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the...

Sensitivity to sequencing depth in single-cell cancer genomics

BackgroundQuerying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the...

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Here we present the Cancer Genome Interpreter, a versatile platform that automates the interpretation of newly sequenced cancer genomes, annotating the potential of alterations detected in tumors to act as...

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for...

Endophenotypes in psychiatric disease: prospects and challenges

Editorial summaryEndophenotypes, quantitative neurobehavioral traits that index genetic susceptibility for a psychiatric disorder, have been examined in thousands of studies. Nevertheless, they have underexploited potential to provide etiological insights into prognosis, how psychopathology develops, the etiology of comorbidity, and the mechanisms of gene function.

Calcitonin gene-related peptide (receptor) antibodies: an exciting avenue for migraine treatment

Editorial summarySpecific prophylactic migraine treatments are urgently needed because of the unmet needs of many migraine patients. Antibodies targeting calcitonin gene-related peptide (CGRP) or its receptor have recently shown efficacy in episodic and chronic migraine and will be available soon.