Articles

The clinical significance of snail protein expression in gastric cancer: a meta-analysis

Snail is a typical transcription factor that could induce epithelial-mesenchymal transition (EMT) and cancer progression. There are some related reports about the clinical significance of snail protein express...

Authors: Xiaoya Chen, Jinjun Li, Ling Hu, William Yang, Lili Lu, Hongyan Jin, Zexiong Wei, Jack Y. Yang, Hamid R. Arabnia, Jun S. Liu, Mary Qu Yang and Youping Deng

A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis

Innumerable opportunities for new genomic research have been stimulated by advancement in high-throughput next-generation sequencing (NGS). However, the pitfall of NGS data abundance is the complication of dis...

Authors: Isaac Akogwu, Nan Wang, Chaoyang Zhang and Ping Gong

Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia

Methylation changes are frequent in cancers, but understanding how hyper- and hypomethylated region changes coordinate, associate with genomic features, and affect gene expression is needed to better understan...

Authors: Garima Kushwaha, Mikhail Dozmorov, Jonathan D. Wren, Jing Qiu, Huidong Shi and Dong Xu

Identification of protein complexes from multi-relationship protein interaction networks

Protein complexes play an important role in biological processes. Recent developments in experiments have resulted in the publication of many high-quality, large-scale protein-protein interaction (PPI) dataset...

Authors: Xueyong Li, Jianxin Wang, Bihai Zhao, Fang-Xiang Wu and Yi Pan

Exome sequencing discloses KALRN homozygous variant as likely cause of intellectual disability and short stature in a consanguineous pedigree

The recent availability of whole-exome sequencing has opened new possibilities for the evaluation of individuals with genetically undiagnosed intellectual disability.

Authors: Periklis Makrythanasis, Michel Guipponi, Federico A. Santoni, Maha Zaki, Mahmoud Y. Issa, Muhammad Ansar, Hanan Hamamy and Stylianos E. Antonarakis

Letter to the editor for “Update of the human and mouse Fanconi anemia genes”

Authors: Daniel W. Nebert, Hongbin Dong, Elspeth A. Bruford, David C. Thompson, Hans Joenje and Vasilis Vasiliou

Experience of a multidisciplinary task force with exome sequencing for Mendelian disorders

In order to optimally integrate the use of high-throughput sequencing (HTS) as a tool in clinical diagnostics of likely monogenic disorders, we have created a multidisciplinary “Genome Clinic Task Force” at th...

Authors: S. Fokstuen, P. Makrythanasis, E. Hammar, M. Guipponi, E. Ranza, K. Varvagiannis, F. A. Santoni, M. Albarca-Aguilera, M. E. Poleggi, F. Couchepin, C. Brockmann, A. Mauron, S. A. Hurst, C. Moret, C. Gehrig, A. Vannier…

AMD and the alternative complement pathway: genetics and functional implications

Age-related macular degeneration (AMD) is an ocular neurodegenerative disorder and is the leading cause of legal blindness in Western societies, with a prevalence of up to 8 % over the age of 60, which continu...

Authors: Perciliz L. Tan, Catherine Bowes Rickman and Nicholas Katsanis

Proposed nomenclature for microhaplotypes

Microhaplotypes are a new type of genetic marker in forensics and population genetics. A standardized nomenclature is desirable. A simple approach that does not require a central authority for approval is prop...

Authors: Kenneth K. Kidd

Genetic risk factors for restenosis after percutaneous coronary intervention in Kazakh population

After coronary stenting, the risk of developing restenosis is from 20 to 35 %. The aim of the present study is to investigate the association of genetic variation in candidate genes in patients diagnosed with ...

Authors: Elena V. Zholdybayeva, Yerkebulan A. Talzhanov, Akbota M. Aitkulova, Pavel V. Tarlykov, Gulmira N. Kulmambetova, Aisha N. Iskakova, Aliya U. Dzholdasbekova, Olga A. Visternichan, Dana Zh. Taizhanova and Yerlan M. Ramanculov

Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach

Atherosclerosis is one of the common health threats all over the world. It is a complex heritable disease that affects arterial blood vessels. Chronic inflammatory response plays an important role in atherogen...

Authors: Dan Xi, Jinzhen Zhao, Wenyan Lai and Zhigang Guo

Human genome meeting 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder

Authors: A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson, R. Polimanti, J. Gelernter, X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen…

Exploring the interaction among EPHX1, GSTP1, SERPINE2, and TGFB1 contributing to the quantitative traits of chronic obstructive pulmonary disease in Chinese Han population

Currently, the majority of genetic association studies on chronic obstructive pulmonary disease (COPD) risk focused on identifying the individual effects of single nucleotide polymorphisms (SNPs) as well as th...

Authors: Li An, Yingxiang Lin, Ting Yang and Lin Hua

Multiplex SNaPshot—a new simple and efficient CYP2D6 and ADRB1 genotyping method

Reliable, inexpensive, high-throughput genotyping methods are required for clinical trials. Traditional assays require numerous enzyme digestions or are too expensive for large sample volumes. Our objective wa...

Authors: Songtao Ben, Rhonda M. Cooper-DeHoff, Hanna K. Flaten, Oghenero Evero, Tracey M. Ferrara, Richard A. Spritz and Andrew A. Monte

Organization, evolution and functions of the human and mouse Ly6/uPAR family genes

Members of the lymphocyte antigen-6 (Ly6)/urokinase-type plasminogen activator receptor (uPAR) superfamily of proteins are cysteine-rich proteins characterized by a distinct disulfide bridge pattern that creat...

Authors: Chelsea L. Loughner, Elspeth A. Bruford, Monica S. McAndrews, Emili E. Delp, Sudha Swamynathan and Shivalingappa K. Swamynathan

Three-hour analysis of non-invasive foetal sex determination: application of Plexor chemistry

The knowledge of the individual genetic “status” in the prenatal era is particularly relevant in the case of positive family history for genetic diseases, in advanced maternal age and in the general screening ...

Authors: Adalgisa Pietropolli, Maria Vittoria Capogna, Raffaella Cascella, Chiara Germani, Valentina Bruno, Claudia Strafella, Simona Sarta, Carlo Ticconi, Giusy Marmo, Sara Gallaro, Giuliana Longo, Luigi Tonino Marsella, Antonio Novelli, Giuseppe Novelli, Emilio Piccione and Emiliano Giardina

The impact of common polymorphisms in CETP and ABCA1 genes with the risk of coronary artery disease in Saudi Arabians

Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide. Many genetic and environmental risk factors including atherogenic dyslipidemia contribute towards the development of CAD. ...

Authors: Cyril Cyrus, Chittibabu Vatte, Awatif Al-Nafie, Shahanas Chathoth, Rudaynah Al-Ali, Abdullah Al-Shehri, Mohammed Shakil Akhtar, Mohammed Almansori, Fahad Al-Muhanna, Brendan Keating and Amein Al-Ali

Reviewer acknowledgement 2015

The Editors of Human Genomics would like to thank all our reviewers who have contributed to the journal in volume 9 (2015).

Authors: Vasilis Vasiliou

A review of the new HGNC gene family resource

The HUGO Gene Nomenclature Committee (HGNC) approves unique gene symbols and names for human loci. As well as naming genomic loci, we manually curate genes into family sets based on shared characteristics such...

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

Erratum to: Copy number variation in CEP57L1 predisposes to congenital absence of bilateral ACL and PCL ligaments

Authors: Yichuan Liu, Yun Li, Michael E. March, Kenny Nguyen, Kexiang Xu, Fengxiang Wang, Yiran Guo, Brendan Keating, Joseph Glessner, Jiankang Li, Theodore J. Ganley, Jianguo Zhang, Matthew A. Deardorff, Xun Xu and Hakon Hakonarson

The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies

Precision medicine in oncology relies on rapid associations between patient-specific variations and targeted therapeutic efficacy. Due to the advancement of genomic analysis, a vast literature characterizing c...

Authors: Sara E. Patterson, Rangjiao Liu, Cara M. Statz, Daniel Durkin, Anuradha Lakshminarayana and Susan M. Mockus

Genetic studies of Polish migraine patients: screening for causative mutations in four migraine-associated genes

Migraine is the most common neurological disorder, affecting approximately 12 % of the adult population worldwide, caused by both environmental and genetic factors. Three causative genes have been identified i...

Authors: Izabela Domitrz, Michalina Kosiorek, Cezary Żekanowski and Anna Kamińska

Intragraft transcriptional profiling of renal transplant patients with tubular dysfunction reveals mechanisms underlying graft injury and recovery

Proximal tubular dysfunction (PTD) is associated with a decreased long-term graft survival in renal transplant patients and can be detected by the elevation of urinary tubular proteins. This study investigated...

Authors: Hátylas Azevedo, Paulo Guilherme Renesto, Rogério Chinen, Erika Naka, Ana Cristina Carvalho de Matos, Marcos Antônio Cenedeze, Carlos Alberto Moreira-Filho, Niels Olsen Saraiva Câmara and Alvaro Pacheco-Silva

Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Chronic obstructive pulmonary disease (COPD) is characterized by an irreversible airflow limitation in response to inhalation of noxious stimuli, such as cigarette smoke. However, only 15–20 % smokers manifest...

Authors: Shannon Bruse, Michael Moreau, Yana Bromberg, Jun-Ho Jang, Nan Wang, Hongseok Ha, Maria Picchi, Yong Lin, Raymond J. Langley, Clifford Qualls, Julia Klensney-Tait, Joseph Zabner, Shuguang Leng, Jenny Mao, Steven A. Belinsky, Jinchuan Xing…

Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer

The human APOBEC protein family plays critical but distinct roles in host defense. Recent studies revealed that APOBECs mediate C-to-T mutagenesis in multiple cancers, including breast cancer. It is still uncl...

Authors: Yanfeng Zhang, Ryan Delahanty, Xingyi Guo, Wei Zheng and Jirong Long

Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients

Next-generation sequencing (NGS) has revolutionized genetic research and offers enormous potential for clinical application. Sequencing the exome has the advantage of casting the net wide for all known coding ...

Authors: Eileen C. P. Lim, Maggie Brett, Angeline H. M. Lai, Siew-Peng Lee, Ee-Shien Tan, Saumya S. Jamuar, Ivy S. L. Ng and Ene-Choo Tan

Update of the human and mouse Fanconi anemia genes

Fanconi anemia (FA) is a recessively inherited disease manifesting developmental abnormalities, bone marrow failure, and increased risk of malignancies. Whereas FA has been studied for nearly 90 years, only in...

Authors: Hongbin Dong, Daniel W. Nebert, Elspeth A. Bruford, David C. Thompson, Hans Joenje and Vasilis Vasiliou

Copy number variation in CEP57L1 predisposes to congenital absence of bilateral ACL and PCL ligaments

Absence of the anterior (ACL) or posterior cruciate ligament (PCL) are rare congenital malformations that result in knee joint instability, with a prevalence of 1.7 per 100,000 live births and can be associate...

Authors: Yichuan Liu, Yun Li, Michael E. March, Kenny Nguyen, Kexiang Xu, Fengxiang Wang, Yiran Guo, Brendan Keating, Joseph Glessner, Jiankang Li, Theodore J. Ganley, Jianguo Zhang, Matthew A. Deardorff, Xun Xu and Hakon Hakonarson

HDAC3 role in medication consumption in medication overuse headache patients: a pilot study

Medication overuse headache (MOH) is a common and debilitating disorder characterized by generation, perpetuation, and persistence of intense chronic migraine, caused by overuse of analgesics, triptans, or oth...

Authors: Claudia Pisanu, Stefano Caproni, Donatella Congiu, Letizia M. Cupini, Alessio Squassina, George P. Patrinos, Ilenia Corbelli, Paolo Calabresi, Maria Del Zompo and Paola Sarchielli

Genomics is changing personal healthcare and medicine: the dawn of iPH (individualized preventive healthcare)

This opinion piece focuses on the convergence of information technology (IT) in the form of personal monitors, especially smart phones and possibly also smart watches, individual genomic information and preven...

Authors: Ruty Mehrian-Shai and Juergen K. V. Reichardt

A survey of computational tools for downstream analysis of proteomic and other omic datasets

Proteomics is an expanding area of research into biological systems with significance for biomedical and therapeutic applications ranging from understanding the molecular basis of diseases to testing new treat...

Authors: Anis Karimpour-Fard, L. Elaine Epperson and Lawrence E. Hunter

Cancer classification in the genomic era: five contemporary problems

Classification is an everyday instinct as well as a full-fledged scientific discipline. Throughout the history of medicine, disease classification is central to how we develop knowledge, make diagnosis, and as...

Authors: Qingxuan Song, Sofia D. Merajver and Jun Z. Li

Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype

The CpG island methylator phenotype (CIMP) was first characterized in colorectal cancer but since has been extensively studied in several other tumor types such as breast, bladder, lung, and gastric. CIMP is o...

Authors: Matahi Moarii, Fabien Reyal and Jean-Philippe Vert

Remotely acting SMCHD1 gene regulatory elements: in silico prediction and identification of potential regulatory variants in patients with FSHD

Facioscapulohumeral dystrophy (FSHD) is commonly associated with contraction of the D4Z4 macro-satellite repeat on chromosome 4q35 (FSHD1) or mutations in the SMCHD1 gene (FSHD2). Recent studies have shown that t...

Authors: Mary B. Mayes, Taniesha Morgan, Jincy Winston, Daniel S. Buxton, Mihir Anant Kamat, Debbie Smith, Maggie Williams, Rebecca L. Martin, Dirk A. Kleinjan, David N. Cooper, Meena Upadhyaya and Nadia Chuzhanova

Eyeing the Cyr61/CTGF/NOV (CCN) group of genes in development and diseases: highlights of their structural likenesses and functional dissimilarities

“CCN” is an acronym referring to the first letter of each of the first three members of this original group of mammalian functionally and phylogenetically distinct extracellular matrix (ECM) proteins [i.e., cy...

Authors: Izabela Krupska, Elspeth A. Bruford and Brahim Chaqour

MATWIN: bridging the gap between academic research and industry

MATWIN (Maturation and Accelerating Translation With INdustry) is part of the nationwide effort to support cancer innovation. This unique program is willing to support innovative research projects providing to...

Authors: Josy Reiffers and Lucia Robert

Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma

Esophageal adenocarcinoma (EA) is among the leading causes of cancer mortality, especially in developed countries. A high level of somatic copy number alterations (CNAs) accumulates over the decades in the pro...

Authors: Xiaoyu Wang, Xiaohong Li, Yichen Cheng, Xin Sun, Xibin Sun, Steve Self, Charles Kooperberg and James Y. Dai

Trans-species polymorphism in humans and the great apes is generally maintained by balancing selection that modulates the host immune response

Known examples of ancient identical-by-descent genetic variants being shared between evolutionarily related species, known as trans-species polymorphisms (TSPs), result from counterbalancing selective forces a...

Authors: Luisa Azevedo, Catarina Serrano, Antonio Amorim and David N. Cooper

Performance evaluation of indel calling tools using real short-read data

Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. With the advance of next-generation sequencing technology, many i...

Authors: Mohammad Shabbir Hasan, Xiaowei Wu and Liqing Zhang

Whole-genome sequencing targets drug-resistant bacterial infections

During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying princ...

Authors: N. V. Punina, N. M. Makridakis, M. A. Remnev and A. F. Topunov

Predicting the combined effect of multiple genetic variants

Many genetic variants have been identified in the human genome. The functional effects of a single variant have been intensively studied. However, the joint effects of multiple variants in the same genes have ...

Authors: Mingming Liu, Layne T. Watson and Liqing Zhang

Epigenetic inheritance and the missing heritability

Genome-wide association studies of complex physiological traits and diseases consistently found that associated genetic factors, such as allelic polymorphisms or DNA mutations, only explained a minority of the...

Authors: Marco Trerotola, Valeria Relli, Pasquale Simeone and Saverio Alberti

Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies

Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated th...

Authors: Boon-Peng Hoh, Lian Deng, Mat Jusoh Julia-Ashazila, Zakaria Zuraihan, Ma’amor Nur-Hasnah, Ab Rajab Nur‐Shafawati, Wan Isa Hatin, Ismail Endom, Bin Alwi Zilfalil, Yusoff Khalid and Shuhua Xu

Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death

Conditions associated with sudden cardiac arrest/death (SCA/D) in youth often have a genetic etiology. While SCA/D is uncommon, a pro-active family screening approach may identify these inherited structural an...

Authors: Mindy H. Li, Jenica L. Abrudan, Matthew C. Dulik, Ariella Sasson, Joshua Brunton, Vijayakumar Jayaraman, Noreen Dugan, Danielle Haley, Ramakrishnan Rajagopalan, Sawona Biswas, Mahdi Sarmady, Elizabeth T. DeChene, Matthew A. Deardorff, Alisha Wilkens, Sarah E. Noon, Maria I. Scarano…

SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing

SIRT1 is likely to play a role in the extension in healthspan induced by dietary restriction. Actions of SIRT1 are pleiotropic, and effects on healthspan may include effects on DNA methylation. Polycomb group ...

Authors: Luisa A Wakeling, Laura J Ions, Suzanne M Escolme, Simon J Cockell, Tianhong Su, Madhurima Dey, Emily V Hampton, Gail Jenkins, Linda J Wainwright, Jill A McKay and Dianne Ford

Genomics in the renal clinic - translating nephrogenetics for clinical practice

Genetic Renal Disease (GRD) presents to mainstream clinicians as a mixture of kidney-specific as well as multi-organ entities, many with highly variable phenotype-genotype relationships. The rapid increase in ...

Authors: Andrew Mallett, Christopher Corney, Hugh McCarthy, Stephen I. Alexander and Helen Healy

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

Cancer, like many common disorders, has a complex etiology, often with a strong genetic component and with multiple environmental factors contributing to susceptibility. A considerable number of genomic varian...

Authors: Ioannis Karageorgos, Clint Mizzi, Efstathia Giannopoulou, Cristiana Pavlidis, Brock A. Peters, Zoi Zagoriti, Peter D. Stenson, Konstantinos Mitropoulos, Joseph Borg, Haralabos P. Kalofonos, Radoje Drmanac, Andrew Stubbs, Peter van der Spek, David N. Cooper, Theodora Katsila and George P. Patrinos

Success stories in genomic medicine from resource-limited countries

In recent years, the translation of genomic discoveries into mainstream medical practice and public health has gained momentum, facilitated by the advent of new technologies. However, there are often major dis...

Authors: Konstantinos Mitropoulos, Hayat Al Jaibeji, Diego A. Forero, Paul Laissue, Ambroise Wonkam, Catalina Lopez-Correa, Zahurin Mohamed, Wasun Chantratita, Ming Ta Michael Lee, Adrian Llerena, Angela Brand, Bassam R. Ali and George P. Patrinos

Clinical application of next-generation sequencing for Mendelian diseases

Over the past decade, next-generation sequencing (NGS) has led to an exponential increase in our understanding of the genetic basis of Mendelian diseases. NGS allows for the analysis of multiple regions of the...

Authors: Saumya Shekhar Jamuar and Ene-Choo Tan

Is the genomic translational pipeline being disrupted?

The translational pipeline for genomic medicine has been well defined. However, as with any rapidly changing technology, innovations are difficult to predict leading to the potential to disrupt anticipated tra...

Authors: Marc S. Williams