Articles

Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization

Human T cell leukemia virus type 1 (HTLV-1) causes adult T cell leukemia (ATL) in a proportion of infected individuals after a long latency period. Development of ATL is a multistep clonal process that can be ...

Authors: Amir Farmanbar, Sanaz Firouzi, Wojciech Makałowski, Masako Iwanaga, Kaoru Uchimaru, Atae Utsunomiya, Toshiki Watanabe and Kenta Nakai

Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology

Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the...

Authors: Ana Lígia Buzolin, Caroline Mônaco Moreira, Patricia Rossi Sacramento, Andre Yuji Oku, Alexandre Ricardo dos Santos Fornari, David Santos Marco Antonio, Caio Robledo D Angioli Costa Quaio, Wagner Rosa Baratela and Miguel Mitne-Neto

The NF1 somatic mutational landscape in sporadic human cancers

Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in...

Authors: Charlotte Philpott, Hannah Tovell, Ian M. Frayling, David N. Cooper and Meena Upadhyaya

Genetic variation in neurodegenerative diseases and its accessibility in the model organism Caenorhabditis elegans

Neurodegenerative diseases (NGDs) such as Alzheimer’s and Parkinson’s are debilitating and largely untreatable conditions strongly linked to age. The clinical, neuropathological, and genetic components of NGDs...

Authors: Yiru Anning Wang, Jan Edward Kammenga and Simon Crawford Harvey

A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets

The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and pr...

Authors: Teresa Requena, Alvaro Gallego-Martinez and Jose A. Lopez-Escamez

Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics

Genetic variant effect prediction algorithms are used extensively in clinical genomics and research to determine the likely consequences of amino acid substitutions on protein function. It is vital that we bet...

Authors: Khalid Mahmood, Chol-hee Jung, Gayle Philip, Peter Georgeson, Jessica Chung, Bernard J. Pope and Daniel J. Park

Identification of novel genes associated with HIV-1 latency by analysis of histone modifications

A reservoir of HIV-1 is a major obstacle in eliminating HIV-1 in patients because it can reactivate in stopping antiretroviral therapy (ART). Histone modifications, such as acetylation and methylation, play a ...

Authors: Kyung-Chang Kim, Sunyoung Lee, Junseock Son, Younghyun Shin, Cheol-Hee Yoon, Chun Kang and Byeong-Sun Choi

Genome-wide DNA methylation analysis reveals hypomethylation in the low-CpG promoter regions in lymphoblastoid cell lines

Epidemiological studies of DNA methylation profiles may uncover the molecular mechanisms through which genetic and environmental factors contribute to the risk of multifactorial diseases. There are two types o...

Authors: Itsuki Taniguchi, Chihiro Iwaya, Keizo Ohnaka, Hiroki Shibata and Ken Yamamoto

In silico prioritization and further functional characterization of SPINK1 intronic variants

SPINK1 (serine protease inhibitor, kazal-type, 1), which encodes human pancreatic secretory trypsin inhibitor, is one of the most extensively studied genes underlying chronic pancreati...

Authors: Wen-Bin Zou, Hao Wu, Arnaud Boulling, David N. Cooper, Zhao-Shen Li, Zhuan Liao, Jian-Min Chen and Claude Férec

Whole-exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera

Polycythemia vera (PV), characterized by massive production of erythrocytes, is one of the myeloproliferative neoplasms. Most patients carry a somatic gain-of-function mutation in JAK2, c.1849G > T (p.Val617Phe),...

Authors: Elina A. M. Hirvonen, Esa Pitkänen, Kari Hemminki, Lauri A. Aaltonen and Outi Kilpivaara

The Israeli National Genetic database: a 10-year experience

The Israeli National and Ethnic Mutation database (http://​server.​goldenhelix.​org/​israeli) was launched in September 2006 on the ETHNOS software to incl...

Authors: Joël Zlotogora and George P. Patrinos

Transcriptome analysis of bronchoalveolar lavage fluid from children with severe Mycoplasma pneumoniae pneumonia reveals novel gene expression and immunodeficiency

A growing number of severe Mycoplasma pneumoniae pneumonia (MPP) cases have been reported recently. However, the pathogenesis of severe MPP is not clear. In the current study, transcriptome sequencing was used to...

Authors: Kuo Wang, Man Gao, Mingyue Yang, Fanzheng Meng, Deli Li, Ruihua Lu, Yan Wang, Huadong Zhuang, Mengyao Li, Genhong Cheng and Xiaosong Wang

Genetic determinants of clinical heterogeneity of the coronary artery disease in the population of Hyderabad, India

Genetic predisposition to the clinical categories of coronary artery disease (anatomical viz., insignificant, single, double, and triple vessel diseases and phenotypic severity categories viz., angina, acute c...

Authors: Rayabarapu Pranavchand, Arramraju Sreenivas Kumar and Battini Mohan Reddy

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity

Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number var...

Authors: Danielle Carpenter, Laura M. Mitchell and John A. L. Armour

Variants in congenital hypogonadotrophic hypogonadism genes identified in an Indonesian cohort of 46,XY under-virilised boys

Congenital hypogonadotrophic hypogonadism (CHH) and Kallmann syndrome (KS) are caused by disruption to the hypothalamic-pituitary-gonadal (H-P-G) axis. In particular, reduced production, secretion or action of...

Authors: Katie L. Ayers, Aurore Bouty, Gorjana Robevska, Jocelyn A. van den Bergen, Achmad Zulfa Juniarto, Nurin Aisyiyah Listyasari, Andrew H. Sinclair and Sultana M. H. Faradz

The status of Her2 amplification and Kras mutations in mucinous ovarian carcinoma

Jayson GC et al. remarked in Lancet that nearly 100% of mucinous ovarian cancer cases have Kras mutation as well as a high frequency of Her2 amplification. Using the Abbott PathVysion Her2 DNA Probe Kit and Kras ...

Authors: Kuang-Leei Chang, Ming-Yung Lee, Wan-Ru Chao and Chih-Ping Han

Head-and-neck squamous cell carcinoma risk in smokers: no association detected between phenotype and AHR, CYP1A1, CYP1A2, or CYP1B1 genotype

Head-and-neck squamous cell carcinoma (HNSCC) differs between smokers and nonsmokers in etiology and clinical presentation. Because of demonstrated unequivocal involvement in smoking-induced cancer in laborato...

Authors: Lucia F. Jorge-Nebert, Ge Zhang, Keith M. Wilson, Zhengwen Jiang, Randall Butler, Jack L. Gluckman, Susan M. Pinney and Daniel W. Nebert

Targeted next generation sequencing identifies novel NOTCH3 gene mutations in CADASIL diagnostics patients

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a monogenic, hereditary, small vessel disease of the brain causing stroke and vascular dementia in adults...

Authors: Neven Maksemous, Robert A. Smith, Larisa M. Haupt and Lyn R. Griffiths

Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD

Autosomal dominant polycystic kidney disease (ADPKD) causes progressive loss of renal function in adults as a consequence of the accumulation of cysts. ADPKD is the most common genetic cause of end-stage renal...

Authors: Rita M. C. de Almeida, Sherry G. Clendenon, William G. Richards, Michael Boedigheimer, Michael Damore, Sandro Rossetti, Peter C. Harris, Britney-Shea Herbert, Wei Min Xu, Angela Wandinger-Ness, Heather H. Ward, James A. Glazier and Robert L. Bacallao

A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease

Genome-wide profiling of rare tumors is crucial for improvement of diagnosis, treatment, and, consequently, achieving better outcomes. Desmoplastic small round cell tumor (DSRCT) is a rare type of sarcoma aris...

Authors: Elisa Napolitano Ferreira, Bruna Durães Figueiredo Barros, Jorge Estefano de Souza, Renan Valieris Almeida, Giovana Tardin Torrezan, Sheila Garcia, Ana Cristina Victorino Krepischi, Celso Abdon Lopes de Mello, Isabela Werneck da Cunha, Clóvis Antonio Lopes Pinto, Fernando Augusto Soares, Emmanuel Dias-Neto, Ademar Lopes, Sandro José de Souza and Dirce Maria Carraro

Navigating the dynamic landscape of long noncoding RNA and protein-coding gene annotations in GENCODE

Our understanding of the transcriptional potential of the genome and its functional consequences has undergone a significant change in the last decade. This has been largely contributed by the improvements in ...

Authors: Saakshi Jalali, Shrey Gandhi and Vinod Scaria

Novel genetic risk variants for pediatric celiac disease

Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-m...

Authors: Angeliki Balasopoulou, Biljana Stanković, Angeliki Panagiotara, Gordana Nikčevic, Brock A. Peters, Anne John, Effrosyni Mendrinou, Apostolos Stratopoulos, Aigli Ioanna Legaki, Vasiliki Stathakopoulou, Aristoniki Tsolia, Nikolaos Govaris, Sofia Govari, Zoi Zagoriti, Konstantinos Poulas, Maria Kanariou…

An efficient method for protein function annotation based on multilayer protein networks

Accurate annotation of protein functions is still a big challenge for understanding life in the post-genomic era. Many computational methods based on protein-protein interaction (PPI) networks have been propos...

Authors: Bihai Zhao, Sai Hu, Xueyong Li, Fan Zhang, Qinglong Tian and Wenyin Ni

A first-line diagnostic assay for limb-girdle muscular dystrophy and other myopathies

Fifty random genetically unstudied families (limb-girdle muscular dystrophy (LGMD)/myopathy) were screened with a gene panel incorporating 759 OMIM genes associated with neurological disorders. Average coverag...

Authors: Dorota Monies, Hindi N. Alhindi, Mohamed A. Almuhaizea, Mohamed Abouelhoda, Anas M. Alazami, Ewa Goljan, Banan Alyounes, Dyala Jaroudi, Abdulelah AlIssa, Khalid Alabdulrahman, Shazia Subhani, Mohamed El-Kalioby, Tariq Faquih, Salma M. Wakil, Nada A. Altassan, Brian F. Meyer…

Variation of global DNA methylation levels with age and in autistic children

The change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the diff...

Authors: Shui-Ying Tsang, Tanveer Ahmad, Flora W. K. Mat, Cunyou Zhao, Shifu Xiao, Kun Xia and Hong Xue

Major influence of repetitive elements on disease-associated copy number variants (CNVs)

Copy number variants (CNVs) are important contributors to the human pathogenic genetic diversity as demonstrated by a number of cases reported in the literature. The high homology between repetitive elements m...

Authors: Ana R. Cardoso, Manuela Oliveira, Antonio Amorim and Luisa Azevedo

MicroRNAs in acute kidney injury

Acute kidney injury (AKI) is an important clinical issue that is associated with significant morbidity and mortality. Despite research advances over the past decades, the complex pathophysiology of AKI is not ...

Authors: Pei-Chun Fan, Chia-Chun Chen, Yung-Chang Chen, Yu-Sun Chang and Pao-Hsien Chu

Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns

Periodontitis is the most common chronic inflammatory disease caused by complex interaction between the microbial biofilm and host immune responses. In the present study, high-throughput RNA sequencing was uti...

Authors: Yong-Gun Kim, Minjung Kim, Ji Hyun Kang, Hyo Jeong Kim, Jin-Woo Park, Jae-Mok Lee, Jo-Young Suh, Jae-Young Kim, Jae-Hyung Lee and Youngkyun Lee

Mutation analysis of the COL1A1 and COL1A2 genes in Vietnamese patients with osteogenesis imperfecta

The genetics of osteogenesis imperfecta (OI) have not been studied in a Vietnamese population before. We performed mutational analysis of the COL1A1 and COL1A2 genes in 91 unrelated OI patients of Vietnamese orig...

Authors: Binh Ho Duy, Lidiia Zhytnik, Katre Maasalu, Ivo Kändla, Ele Prans, Ene Reimann, Aare Märtson and Sulev Kõks

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

Association of six CpG-SNPs in the inflammation-related genes with coronary heart disease

Chronic inflammation has been widely considered to be the major risk factor of coronary heart disease (CHD). The goal of our study was to explore the possible association with CHD for inflammation-related sing...

Authors: Xiaomin Chen, Xiaoying Chen, Yan Xu, William Yang, Nan Wu, Huadan Ye, Jack Y. Yang, Qingxiao Hong, Yanfei Xin, Mary Qu Yang, Youping Deng and Shiwei Duan

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

The up-regulation of Myb may help mediate EGCG inhibition effect on mouse lung adenocarcinoma

Green tea polyphenol epigallocatechin-3-gallate (EGCG) has been demonstrated to inhibit cancer in experimental studies through its antioxidant activity and modulations on cellular functions by binding specific...

Authors: Hong Zhou, Joseph Manthey, Ekaterina Lioutikova, William Yang, Kenji Yoshigoe, Mary Qu Yang and Hong Wang

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