Articles

Exome sequencing identifies novel and recurrent mutations in GJA8 and CRYGDassociated with inherited cataract

Inherited cataract is a clinically important and genetically heterogeneous cause of visual impairment. Typically, it presents at an early age with or without other ocular/systemic signs and lacks clear phenoty...

Authors: Donna S Mackay, Thomas M Bennett, Susan M Culican and Alan Shiels

Informed consent and ethical re-use of African genomic data

Rapid advances in human genomic research are increasing the availability of genomic data for secondary analysis. Particularly in the case of vulnerable African populations, ethics and informed consent processe...

Authors: Galen EB Wright, Adebowale A Adeyemo and Nicki Tiffin

Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease

Biological systems are exquisitely poised to respond and adjust to challenges, including damage. However, sustained damage can overcome the ability of the system to adjust and result in a disease phenotype, it...

Authors: Victoria Petri, G Thomas Hayman, Marek Tutaj, Jennifer R Smith, Stanley JF Laulederkind, Shur-Jen Wang, Rajni Nigam, Jeff De Pons, Mary Shimoyama, Melinda R Dwinell, Elizabeth A Worthey and Howard J Jacob

Improved drug therapy: triangulating phenomics with genomics and metabolomics

Embracing the complexity of biological systems has a greater likelihood to improve prediction of clinical drug response. Here we discuss limitations of a singular focus on genomics, epigenomics, proteomics, tr...

Authors: Andrew A Monte, Chad Brocker, Daniel W Nebert, Frank J Gonzalez, David C Thompson and Vasilis Vasiliou

Ethical issues in genomic research on the African continent: experiences and challenges to ethics review committees

This is a report on a workshop titled ‘Ethics for genomic research across five African countries: Guidelines, experiences and challenges’, University of the Witwatersrand, Johannesburg, South Africa, 10 and 11...

Authors: Michèle Ramsay, Jantina de Vries, Himla Soodyall, Shane A Norris and Osman Sankoh

Mixture models for gene expression experiments with two species

Cross-species research in drug development is novel and challenging. A bivariate mixture model utilizing information across two species was proposed to solve the fundamental problem of identifying differential...

Authors: Yuhua Su, Lei Zhu, Alan Menius and Jason Osborne

Validation and assessment of variant calling pipelines for next-generation sequencing

The processing and analysis of the large scale data generated by next-generation sequencing (NGS) experiments is challenging and is a burgeoning area of new methods development. Several new bioinformatics tool...

Authors: Mehdi Pirooznia, Melissa Kramer, Jennifer Parla, Fernando S Goes, James B Potash, W Richard McCombie and Peter P Zandi

Radiation-induced myeloid leukemia in murine models

The use of radiation therapy is a cornerstone of modern cancer treatment. The number of patients that undergo radiation as a part of their therapy regimen is only increasing every year, but this does not come ...

Authors: Leena Rivina, Michael Davoren and Robert H Schiestl

Ranking non-synonymous single nucleotide polymorphisms based on disease concepts

As the number of non-synonymous single nucleotide polymorphisms (nsSNPs) identified through whole-exome/whole-genome sequencing programs increases, researchers and clinicians are becoming increasingly reliant ...

Authors: Hashem A Shihab, Julian Gough, Matthew Mort, David N Cooper, Ian NM Day and Tom R Gaunt

Novel age-dependent targets in vestibular schwannomas

Schwannomas are the most common neurofibromatosis type 2 (NF2)-associated tumors with significant phenotypic heterogeneity in patients. The most severe subtype has an early and rapid progression and the mild t...

Authors: Amos Toren, Juergen K Reichardt, Ali Andalibi, Nancy Ya-Hsuan Hsu, Joni Doherty, William Slattery and Ruty Mehrian-Shai

Changing genetic paradigms: creating next-generation genetic databases as tools to understand the emerging complexities of genotype/phenotype relationships

Understanding genotype/phenotype relationships has become more complicated as increasing amounts of inter- and intra-tissue genetic heterogeneity have been revealed through next-generation sequencing and evide...

Authors: Bruce Gottlieb, Lenore K Beitel and Mark Trifiro

QGRS-Conserve: a computational method for discovering evolutionarily conserved G-quadruplex motifs

Nucleic acids containing guanine tracts can form quadruplex structures via non-Watson-Crick base pairing. Formation of G-quadruplexes is associated with the regulation of important biological functions such as...

Authors: Scott Frees, Camille Menendez, Matt Crum and Paramjeet S Bagga

A short guide to long non-coding RNA gene nomenclature

The HUGO Gene Nomenclature Committee (HGNC) is the only organisation authorised to assign standardised nomenclature to human genes. Of the 38,000 approved gene symbols in our database (

Authors: Mathew W Wright

A tissue-specific gene expression template portrays heart development and pathology

Congenital heart defects (CHD) are the most common cause of death in children under the age of 1. Tetralogy of Fallot (TOF) is a severe CHD that results from developmental defects in the conotruncal outflow tr...

Authors: Amy Rodemoyer, Nataliya Kibiryeva, Alexis Bair, Jennifer Marshall, James E O’Brien Jr and Douglas C Bittel

A gene-specific non-enhancer sequence is critical for expression from the promoter of the small heat shock protein gene αB-crystallin

Deciphering of the information content of eukaryotic promoters has remained confined to universal landmarks and conserved sequence elements such as enhancers and transcription factor binding motifs, which are ...

Authors: Zhe Jing, Rajendra K Gangalum, Dennis C Mock and Suraj P Bhat

Forced swim test induces divergent global transcriptomic alterations in the hippocampus of high versus low novelty-seeker rats

Many neuropsychiatric disorders, including stress-related mood disorders, are complex multi-parametric syndromes. Susceptibility to stress and depression is individually different. The best animal model of ind...

Authors: Pothitos M Pitychoutis, Despina Sanoudou, Margarita Papandreou, Dimitris Nasias, Marianna Kouskou, Craig R Tomlinson, Panagiotis A Tsonis and Zeta Papadopoulou-Daifoti

Reviewer acknowledgement 2014

The Editors of Human Genomics would like to thank all our reviewers who have contributed to the journal in volume 7 (2013).

Authors: Vasilis Vasiliou

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data

Alternative splicing is a major contributor to cellular diversity. Therefore the identification and quantification of differentially spliced transcripts in genome-wide transcript analysis is an important consi...

Authors: Joan E Hooper

On the stability of the Bayenv method in assessing human SNP-environment associations

Phenotypic variation along environmental gradients has been documented among and within many species, and in some cases, genetic variation has been shown to be associated with these gradients. Bayenv is a rela...

Authors: Lily M Blair, Julie M Granka and Marcus W Feldman

A study of the role of GATA4 polymorphism in cardiovascular metabolic disorders

The study was designed to evaluate the association of GATA4 gene polymorphism with coronary artery disease (CAD) and its metabolic risk factors, including dyslipidaemic disorders, obesity, type 2 diabetes and hyp...

Authors: Nzioka P Muiya, Salma M Wakil, Asma I Tahir, Samya Hagos, Mohammed Najai, Daisy Gueco, Nada Al-Tassan, Editha Andres, Nejat Mazher, Brian F Meyer and Nduna Dzimiri

Transcriptomics to study the effect of a Mediterranean-inspired diet on inflammation in Crohn's disease patients

Inflammation is an essential immune response; however, chronic inflammation results in disease including Crohn's disease. Therefore, reducing the inflammation can yield a significant health benefit, and one wa...

Authors: Gareth Marlow, Stephanie Ellett, Isobel R Ferguson, Shuotun Zhu, Nishi Karunasinghe, Amalini C Jesuthasan, Dug Yeo Han, Alan G Fraser and Lynnette R Ferguson

Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data

Up to 20% of cancers worldwide are thought to be associated with microbial pathogens, including bacteria and viruses. The widely used methods of viral infection detection are usually limited to a few a priori sus...

Authors: Daria Salyakina and Nicholas F Tsinoremas

Update of the human and mouse SERPINgene superfamily

The serpin family comprises a structurally similar, yet functionally diverse, set of proteins. Named originally for their function as serine proteinase inhibitors, many of its members are not inhibitors but ra...

Authors: Claire Heit, Brian C Jackson, Monica McAndrews, Mathew W Wright, David C Thompson, Gary A Silverman, Daniel W Nebert and Vasilis Vasiliou

CER1gene variations associated with bone mineral density, bone markers, and early menopause in postmenopausal women

Osteoporosis has a multifactorial pathogenesis characterized by a combination of low bone mass and increased fragility. In our study, we focused on the effects of polymorphisms in CER1 and DKK1 genes, recently re...

Authors: Theodora Koromila, Panagiotis Georgoulias, Zoe Dailiana, Evangelia E Ntzani, Stavroula Samara, Chris Chassanidis, Vassiliki Aleporou-Marinou and Panagoula Kollia

K-Map: connecting kinases with therapeutics for drug repurposing and development

Protein kinases play important roles in regulating signal transduction in eukaryoticcells. Due to evolutionary conserved binding sites in the catalytic domain of thekinases, most inhibitors that target these s...

Authors: Jihye Kim, Minjae Yoo, Jaewoo Kang and Aik Choon Tan

Role of conserved cis-regulatory elements in the post-transcriptional regulation of the human MECP2 gene involved in autism

The MECP2 gene codes for methyl CpG binding protein 2 which regulates activities of other genes in the early development of the brain. Mutations in this gene have been associated with Rett syndrome, a form of ...

Authors: Joetsaroop S Bagga and Lawrence A D’Antonio

Screening in silico predicted remotely acting NF1gene regulatory elements for mutations in patients with neurofibromatosis type 1

Neurofibromatosis type 1 (NF1), a neuroectodermal disorder, is caused by germline mutations in the NF1 gene. NF1 affects approximately 1/3,000 individuals worldwide, with about 50% of cases representing de novo m...

Authors: Stephen E Hamby, Pablo Reviriego, David N Cooper, Meena Upadhyaya and Nadia Chuzhanova

Genetic tests obtainable through pharmacies: the good, the bad, and the ugly

Genomic medicine seeks to exploit an individual’s genomic information in the context of guiding the clinical decision-making process. In the post-genomic era, a range of novel molecular genetic testing methodo...

Authors: George P Patrinos, Darrol J Baker, Fahd Al-Mulla, Vasilis Vasiliou and David N Cooper

Rank-based genome-wide analysis reveals the association of Ryanodine receptor-2 gene variants with childhood asthma among human populations

The standard approach to determine unique or shared genetic factors across populations is to identify risk alleles in one population and investigate replication in others. However, since populations differ in ...

Authors: Lili Ding, Tilahun Abebe, Joseph Beyene, Russell A Wilke, Arnon Goldberg, Jessica G Woo, Lisa J Martin, Marc E Rothenberg, Marepalli Rao, Gurjit K Khurana Hershey, Ranajit Chakraborty and Tesfaye B Mersha

New susceptibility locus for obesity and dyslipidaemia on chromosome 3q22.3

The muscle Ras (MRAS) gene resides on chromosome 3q22.3 and encodes a member of the membrane-associated Ras small GTPase proteins, which function as signal transducers in multiple processes including cell growth ...

Authors: Maie Alshahid, Salma M Wakil, Mohammed Al-Najai, Nzioka P Muiya, Samar Elhawari, Daisy Gueco, Editha Andres, Samia Hagos, Nejat Mazhar, Brian F Meyer and Nduna Dzimiri

Comparative study and meta-analysis of meta-analysis studies for the correlation of genomic markers with early cancer detection

A large number of common disorders, including cancer, have complex genetic traits, with multiple genetic and environmental components contributing to susceptibility. A literature search revealed that even amon...

Authors: Zoi Lanara, Efstathia Giannopoulou, Marta Fullen, Evangelos Kostantinopoulos, Jean-Christophe Nebel, Haralabos P Kalofonos, George P Patrinos and Cristiana Pavlidis

Update on the Kelch-like (KLHL) gene family

The Kelch-like (KLHL) gene family encodes a group of proteins that generally possess a BTB/POZ domain, a BACK domain, and five to six Kelch motifs. BTB domains facilitate protein binding and dimerization. The ...

Authors: Bajinder S Dhanoa, Tiziana Cogliati, Akhila G Satish, Elspeth A Bruford and James S Friedman

Vive la différence: naming structural variants in the human reference genome

The HUGO Gene Nomenclature Committee has approved gene symbols for the majority of protein-coding genes on the human reference genome. To adequately represent regions of complex structural variation, the Genom...

Authors: Ruth L Seal, Mathew W Wright, Kristian A Gray and Elspeth A Bruford

Exome sequencing identifies nonsegregating nonsense ATM and PALB2variants in familial pancreatic cancer

We sequenced 11 germline exomes from five families with familial pancreatic cancer (FPC). One proband had a germline nonsense variant in ATM with somatic loss of the variant allele. Another proband had a nonsense...

Authors: Robert C Grant, Wigdan Al-Sukhni, Ayelet E Borgida, Spring Holter, Zaheer S Kanji, Treasa McPherson, Emily Whelan, Stefano Serra, Quang M Trinh, Vanya Peltekova, Lincoln D Stein, John D McPherson and Steven Gallinger

Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach

Recent reports suggest the role of nonsynonymous single nucleotide polymorphisms (nsSNPs) in cyclin-dependent kinase 7 (CDK7) gene associated with defect in the DNA repair mechanism that may contribute to cancer ...

Authors: C George Priya Doss, N Nagasundaram, Chiranjib Chakraborty, Luonan Chen and Hailong Zhu

Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hoxstructure for non-mammalian tetrapod vertebrates?

Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding an...

Authors: Stephen Randal Voss, Srikrishna Putta, John A Walker, Jeramiah J Smith, Nobuyasu Maki and Panagiotis A Tsonis

Genetic effects of ATP1A2 in familial hemiplegic migraine type II and animal models

Na⁺/K⁺-ATPase alpha 2 (Atp1a2) is an integral plasma membrane protein belonging to the P-type ATPase family that is responsible for maintaining the sodium (Na⁺) and potassium (K⁺) gradients across cellular membra...

Authors: Stephanie M Gritz and Richard A Radcliffe

Value that industrial collaborations bring to research and education efforts in universities: perspective of a professor working in the field of development of therapeutic proteins

Authors: John F Carpenter

Development of a cost-effective high-throughput process of microsatellite analysis involving miniaturized multiplexed PCR amplification and automated allele identification

Microsatellites are nucleotide sequences of tandem repeats occurring throughout the genome, which have been widely used in genetic linkage analysis, studies of loss of heterozygosity, determination of lineage ...

Authors: Truc TM Nguyen, Shaheen E Lakhan and Barry A Finette

How to create innovation by building the translation bridge from basic research into medicinal drugs: an industrial perspective

The global healthcare industry is undergoing substantial changes and adaptations to the constant decline of approved new medical entities. This decrease in internal research productivity is resulting in a majo...

Authors: Paul G Germann, Alexander Schuhmacher, Juan Harrison, Ronald Law, Kevin Haug and Gordon Wong

The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information

The RGD Pathway Portal provides pathway annotations for rat, human and mouse genes and pathway diagrams and suites, all interconnected via the pathway ontology. Diagram pages present the diagram and descriptio...

Authors: G Thomas Hayman, Pushkala Jayaraman, Victoria Petri, Marek Tutaj, Weisong Liu, Jeff De Pons, Melinda R Dwinell and Mary Shimoyama

An essential reference for the drug safety practitioner

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Authors: Andrew A Monte

Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data

A bivariate mixture model utilizing information across two species was proposed to solve the fundamental problem of identifying differentially expressed genes in microarray experiments. The model utility was i...

Authors: Yuhua Su, Dahlia Nielsen, Lei Zhu, Kristy Richards, Steven Suter, Matthew Breen, Alison Motsinger-Reif and Jason Osborne

Softwares and methods for estimating genetic ancestry in human populations

The estimation of genetic ancestry in human populations has important applications in medical genetic studies. Genetic ancestry is used to control for population stratification in genetic association studies, ...

Authors: Yushi Liu, Toru Nyunoya, Shuguang Leng, Steven A Belinsky, Yohannes Tesfaigzi and Shannon Bruse

A new era in the discovery of de novomutations underlying human genetic disease

Authors: Chee-Seng Ku, Vasilis Vasiliou and David N Cooper

The human crystallin gene families

Crystallins are the abundant, long-lived proteins of the eye lens. The major human crystallins belong to two different superfamilies: the small heat-shock proteins (α-crystallins) and the βγ-crystallins. Durin...

Authors: Graeme Wistow

16th Carbonyl Metabolism Meeting: from enzymology to genomics

The 16th International Meeting on the Enzymology and Molecular Biology of Carbonyl Metabolism, Castle of Ploen (Schleswig-Holstein, Germany), July 10–15, 2012, covered all aspects of NAD(P)-dependent oxido-red...

Authors: Edmund Maser

Association of genome variations in the renin-angiotensin system with physical performance

The aim of this study was to determine the genotype distribution and allelic frequencies of ACE (I/D), AGTR1 (A +1166 C), BDKRB2 (+9/−9) and LEP (G–2548A) genomic variations in 175 Greek athletes who excelled at ...

Authors: Argyro Sgourou, Vassilis Fotopoulos, Vassilis Kontos, George P Patrinos and Adamantia Papachatzopoulou

An emerging role for microRNAs in NF1 tumorigenesis

MicroRNAs (miRNAs) are a class of non-coding RNA, which have recently been shown to have a wide variety of regulatory functions in relation to gene expression. Since their identification nearly 20 years ago, m...

Authors: Ashni Sedani, David N Cooper and Meena Upadhyaya

Pseudoexfoliation syndrome, a systemic disorder with ocular manifestations

Pseudoexfoliation syndrome (PXS) is a systemic condition with eye manifestations. In the eye, pseudoexfoliation material deposits on various structures of the anterior segment. The nature of this material is m...

Authors: Eman Elhawy, Gautam Kamthan, Cecilia Q Dong and John Danias