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  1. Research article

    Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine

    Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, ther...

    Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T. Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang and Gholson J. Lyon

    BMC Medical Genomics 2017 10:10

    Published on: 23 February 2017

  2. Research article

    Genomic newborn screening: public health policy considerations and recommendations

    The use of genome-wide (whole genome or exome) sequencing for population-based newborn screening presents an opportunity to detect and treat or prevent many more serious early-onset health conditions than is p...

    Jan M. Friedman, Martina C. Cornel, Aaron J. Goldenberg, Karla J. Lister, Karine Sénécal and Danya F. Vears

    BMC Medical Genomics 2017 10:9

    Published on: 21 February 2017

  3. Research article

    Next-generation sequencing in familial breast cancer patients from Lebanon

    Familial breast cancer (BC) represents 5 to 10% of all BC cases. Mutations in two high susceptibility BRCA1 and BRCA2 genes explain 16–40% of familial BC, while other high, moderate and low susceptibility genes e...

    Nadine Jalkh, Eliane Chouery, Zahraa Haidar, Christina Khater, David Atallah, Hamad Ali, Makia J. Marafie, Mohamed R. Al-Mulla, Fahd Al-Mulla and Andre Megarbane

    BMC Medical Genomics 2017 10:8

    Published on: 15 February 2017

  4. Research article

    Multidisciplinary insight into clonal expansion of HTLV-1–infected cells in adult T-cell leukemia via modeling by deterministic finite automata coupled with high-throughput sequencing

    Clonal expansion of leukemic cells leads to onset of adult T-cell leukemia (ATL), an aggressive lymphoid malignancy with a very poor prognosis. Infection with human T-cell leukemia virus type-1 (HTLV-1) is the...

    Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kenta Nakai, Kaoru Uchimaru and Toshiki Watanabe

    BMC Medical Genomics 2017 10:4

    Published on: 31 January 2017

  5. Research article

    Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes

    Type 1 diabetes (T1D) is an autoimmune disease and extensive evidence has indicated a critical role of both the innate and the adaptive arms of immune system in disease development. To date most clinical trial...

    Shouguo Gao, Nathaniel Wolanyk, Ye Chen, Shuang Jia, Martin J. Hessner and Xujing Wang

    BMC Medical Genomics 2017 10:7

    Published on: 31 January 2017

  6. Case report

    Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

    Microcephaly has become a major public health problem in Brazil. The total number of newborns with microcephaly was reported to be >4000 in June 2016. Studies suggest that Zika Virus is a major cause of new mi...

    Diogo Antonio Tschoeke, Louisi Souza de Oliveira, Luciana Leomil, Amilcar Tanuri and Fabiano Lopes Thompson

    BMC Medical Genomics 2017 10:5

    Published on: 11 January 2017

  7. Debate

    Health and genetic ancestry testing: time to bridge the gap

    It is becoming increasingly difficult to keep information about genetic ancestry separate from information about health, and consumers of genetic ancestry tests are becoming more aware of the potential health ...

    Andrew Smart, Deborah A. Bolnick and Richard Tutton

    BMC Medical Genomics 2017 10:3

    Published on: 9 January 2017

  8. Research article

    A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients

    Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are forms of hepatic autoimmunity, and risk for both diseases has a strong genetic component. This study aimed to define the genetic a...

    Agnieszka Paziewska, Andrzej Habior, Agnieszka Rogowska, Włodzimierz Zych, Krzysztof Goryca, Jakub Karczmarski, Michalina Dabrowska, Filip Ambrozkiewicz, Bozena Walewska-Zielecka, Marek Krawczyk, Halina Cichoz-Lach, Piotr Milkiewicz, Agnieszka Kowalik, Krzysztof Mucha, Joanna Raczynska, Joanna Musialik…

    BMC Medical Genomics 2017 10:2

    Published on: 6 January 2017

  9. Research article

    Genetic study of congenital bile-duct dilatation identifies de novo and inherited variants in functionally related genes

    Congenital dilatation of the bile-duct (CDD) is a rare, mostly sporadic, disorder that results in bile retention with severe associated complications. CDD affects mainly Asians. To our knowledge, no genetic st...

    John K. L. Wong, Desmond Campbell, Ngoc Diem Ngo, Fanny Yeung, Guo Cheng, Clara S. M. Tang, Patrick H. Y. Chung, Ngoc Son Tran, Man-ting So, Stacey S. Cherny, Pak C. Sham, Paul K. Tam and Maria-Mercè Garcia-Barcelo

    BMC Medical Genomics 2016 9:75

    Published on: 12 December 2016

  10. Research

    A pilot study on the prevalence of DNA palindromes in breast cancer genomes

    DNA palindromes are a unique pattern of repeat sequences that are present in the human genome. It consists of a sequence of nucleotides in which the second half is the complement of the first half but appearin...

    Sandeep Subramanian, Srilakshmi Chaparala, Viji Avali and Madhavi K. Ganapathiraju

    BMC Medical Genomics 2016 9(Suppl 3):73

    Published on: 5 December 2016

    This article is part of a Supplement: Volume 9 Supplement 3

  11. Research

    Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses

    The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune syste...

    Haifen Chen, Xinrui Zhou, Jie Zheng and Chee-Keong Kwoh

    BMC Medical Genomics 2016 9(Suppl 3):69

    Published on: 5 December 2016

    This article is part of a Supplement: Volume 9 Supplement 3

  12. Research

    GSNFS: Gene subnetwork biomarker identification of lung cancer expression data

    Gene expression has been used to identify disease gene biomarkers, but there are ongoing challenges. Single gene or gene-set biomarkers are inadequate to provide sufficient understanding of complex disease mec...

    Narumol Doungpan, Worrawat Engchuan, Jonathan H. Chan and Asawin Meechai

    BMC Medical Genomics 2016 9(Suppl 3):70

    Published on: 5 December 2016

    This article is part of a Supplement: Volume 9 Supplement 3

  13. Research

    Fuzzy-FishNET: a highly reproducible protein complex-based approach for feature selection in comparative proteomics

    The hypergeometric enrichment analysis approach typically fares poorly in feature-selection stability due to its upstream reliance on the t-test to generate differential protein lists before testing for enrichmen...

    Wilson Wen Bin Goh

    BMC Medical Genomics 2016 9(Suppl 3):67

    Published on: 5 December 2016

    This article is part of a Supplement: Volume 9 Supplement 3

  14. Research

    Gene masking - a technique to improve accuracy for cancer classification with high dimensionality in microarray data

    High dimensional feature space generally degrades classification in several applications. In this paper, we propose a strategy called gene masking, in which non-contributing dimensions are heuristically remove...

    Harsh Saini, Sunil Pranit Lal, Vimal Vikash Naidu, Vincel Wince Pickering, Gurmeet Singh, Tatsuhiko Tsunoda and Alok Sharma

    BMC Medical Genomics 2016 9(Suppl 3):74

    Published on: 5 December 2016

    This article is part of a Supplement: Volume 9 Supplement 3

  15. Research article

    DNA methylation patterns associated with oxidative stress in an ageing population

    Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits...

    Åsa K. Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind and Erik Ingelsson

    BMC Medical Genomics 2016 9:72

    Published on: 25 November 2016

  16. Research article

    “A rising tide lifts all boats”: establishing a multidisciplinary genomic tumor board for breast cancer patients with advanced disease

    Research suggests that multidisciplinary genomic tumor boards (MGTB) can inform cancer patient care, though little is known about factors influencing how MGTBs interpret genomic test results, make recommendati...

    Michelle L. McGowan, Roselle S. Ponsaran, Paula Silverman, Lyndsay N. Harris and Patricia A. Marshall

    BMC Medical Genomics 2016 9:71

    Published on: 21 November 2016

  17. Research article

    A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without

    Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus ...

    Wendy Kröger, Darlington Mapiye, Jean-Baka Domelevo Entfellner and Nicki Tiffin

    BMC Medical Genomics 2016 9:66

    Published on: 15 November 2016

  18. Technical advance

    Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer

    The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since...

    Bernard Omolo, Mingli Yang, Fang Yin Lo, Michael J. Schell, Sharon Austin, Kellie Howard, Anup Madan and Timothy J. Yeatman

    BMC Medical Genomics 2016 9:65

    Published on: 19 October 2016

  19. Research article

    Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing

    The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adeq...

    Lei Wei, Antonios Papanicolau-Sengos, Song Liu, Jianmin Wang, Jeffrey M. Conroy, Sean T. Glenn, Elizabeth Brese, Qiang Hu, Kiersten Marie Miles, Blake Burgher, Maochun Qin, Karen Head, Angela R. Omilian, Wiam Bshara, John Krolewski, Donald L. Trump…

    BMC Medical Genomics 2016 9:64

    Published on: 19 October 2016

  20. Technical advance

    Protecting genomic data analytics in the cloud: state of the art and opportunities

    The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, ...

    Haixu Tang, Xiaoqian Jiang, Xiaofeng Wang, Shuang Wang, Heidi Sofia, Dov Fox, Kristin Lauter, Bradley Malin, Amalio Telenti, Li Xiong and Lucila Ohno-Machado

    BMC Medical Genomics 2016 9:63

    Published on: 13 October 2016

  21. Correspondence

    The Anatomy to Genomics (ATG) Start Genetics medical school initiative: incorporating exome sequencing data from cadavers used for Anatomy instruction into the first year curriculum

    The increasing use of next generation DNA sequencing in clinical medicine is exposing the need for more genetics education in physician training. We piloted an initiative to determine the feasibility of incorp...

    Glenn S. Gerhard, Qunyan Jin, Barbara V. Paynton and Steven N. Popoff

    BMC Medical Genomics 2016 9:62

    Published on: 6 October 2016

  22. Research article

    An adaptive detection method for fetal chromosomal aneuploidy using cell-free DNA from 447 Korean women

    Noninvasive prenatal testing (NIPT) using massively parallel sequencing of cell-free DNA (cfDNA) is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predicti...

    Sunshin Kim, HeeJung Jung, Sung Hee Han, SeungJae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Kyudong Han, Hwanjong Kwak, Sunghoon Park, Hee Jae Joo, Minae An, Jungsu Ha, Kyusang Lee, Byung Chul Kim, Hailing Zheng…

    BMC Medical Genomics 2016 9:61

    Published on: 3 October 2016

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