Prognostics and diagnostics/biomarkers

This section considers studies on the use of genomic markers to diagnose, classify, or predict the risk or prognosis of human disease.

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  1. Case report

    Identification of trunk mutations in gastric carcinoma: a case study

    Intratumor heterogeneity (ITH) poses an urgent challenge for cancer precision medicine because it can cause drug resistance against cancer target therapy and immunotherapy. The search for trunk mutations that ...

    Zhan Zhou, Shanshan Wu, Jun Lai, Yuan Shi, Chixiao Qiu, Zhe Chen, Yufeng Wang, Xun Gu, Jie Zhou and Shuqing Chen

    BMC Medical Genomics 2017 10:49

    Published on: 17 July 2017

  2. Technical advance

    Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing

    The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mu...

    Donavan T. Cheng, Meera Prasad, Yvonne Chekaluk, Ryma Benayed, Justyna Sadowska, Ahmet Zehir, Aijazuddin Syed, Yan Elsa Wang, Joshua Somar, Yirong Li, Zarina Yelskaya, Donna Wong, Mark E. Robson, Kenneth Offit, Michael F. Berger, Khedoudja Nafa…

    BMC Medical Genomics 2017 10:33

    Published on: 19 May 2017

  3. Research article

    Patient complexity and genotype-phenotype correlations in biliary atresia: a cross-sectional analysis

    Biliary Atresia (BA) is rare and genetically complex, and the pathogenesis is elusive. The disease course is variable and can represent heterogeneity, which hinders effective disease management. Deciphering th...

    Guo Cheng, Patrick Ho-Yu Chung, Edwin Kin-Wai Chan, Man-Ting So, Pak-Chung Sham, Stacey S. Cherny, Paul Kwong-Hang Tam and Maria-Mercè Garcia-Barceló

    BMC Medical Genomics 2017 10:22

    Published on: 17 April 2017

  4. Research article

    GRMD cardiac and skeletal muscle metabolism gene profiles are distinct

    Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, which codes for the dystrophin protein. While progress has been made in defining the molecular basis and pathogenesis of DMD, major gaps r...

    Larry W. Markham, Candice L. Brinkmeyer-Langford, Jonathan H. Soslow, Manisha Gupte, Douglas B. Sawyer, Joe N. Kornegay and Cristi L. Galindo

    BMC Medical Genomics 2017 10:21

    Published on: 8 April 2017

  5. Research article

    Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation sequencing

    The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platfor...

    Henry M. Wood, Joseph M. Foster, Morag Taylor, Emma Tinkler-Hundal, Fiona S. Togneri, Paula Wojtowicz, Assa Oumie, Karen G. Spink, Fiona Brew and Philip Quirke

    BMC Medical Genomics 2017 10:17

    Published on: 18 March 2017

  6. Research article

    PALB2 mutations in BRCA1/2-mutation negative breast and ovarian cancer patients from Poland

    The PALB2 gene encodes a protein that plays a crucial role in maintaining genomic integrity. Germline inactivating mutations in PALB2 are associated with an increased risk of breast and ovarian cancer. The preval...

    Anna Kluska, Aneta Balabas, Magdalena Piatkowska, Katarzyna Czarny, Katarzyna Paczkowska, Dorota Nowakowska, Michal Mikula and Jerzy Ostrowski

    BMC Medical Genomics 2017 10:14

    Published on: 9 March 2017

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Research article

    A 19-Gene expression signature as a predictor of survival in colorectal cancer

    Histopathological assessment has a low potential to predict clinical outcome in patients with the same stage of colorectal cancer. More specific and sensitive biomarkers to determine patients’ survival are nee...

    Nurul Ainin Abdul Aziz, Norfilza M. Mokhtar, Roslan Harun, Md Manir Hossain Mollah, Isa Mohamed Rose, Ismail Sagap, Azmi Mohd Tamil, Wan Zurinah Wan Ngah and Rahman Jamal

    BMC Medical Genomics 2016 9:58

    Published on: 8 September 2016

  14. Debate

    Known unknowns: building an ethics of uncertainty into genomic medicine

    Genomic testing has reached the point where, technically at least, it can be cheaper to undertake panel-, exome- or whole genome testing than it is to sequence a single gene. An attribute of these approaches i...

    Ainsley J. Newson, Samantha J. Leonard, Alison Hall and Clara L. Gaff

    BMC Medical Genomics 2016 9:57

    Published on: 1 September 2016

  15. Research article

    Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay

    The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, select...

    Mahesh Iddawela, Oscar M. Rueda, Marcus Klarqvist, Stefan Graf, Helena M. Earl and Carlos Caldas

    BMC Medical Genomics 2016 9:54

    Published on: 20 August 2016

  16. Research article

    Acute appendicitis: transcript profiling of blood identifies promising biomarkers and potential underlying processes

    The diagnosis of acute appendicitis can be surprisingly difficult without computed tomography, which carries significant radiation exposure. Circulating blood cells may carry informative changes in their RNA e...

    Lakhmir S. Chawla, Ian Toma, Danielle Davison, Khashayar Vaziri, Juliet Lee, Raymond Lucas, Michael G. Seneff, Aoibhinn Nyhan and Timothy A. McCaffrey

    BMC Medical Genomics 2016 9:40

    Published on: 15 July 2016

  17. Research Article

    Breast cancer subtype predictors revisited: from consensus to concordance?

    At the molecular level breast cancer comprises a heterogeneous set of subtypes associated with clear differences in gene expression and clinical outcomes. Single sample predictors (SSPs) are built via a two-st...

    Herman MJ. Sontrop, Marcel JT. Reinders and Perry D. Moerland

    BMC Medical Genomics 2016 9:26

    Published on: 3 June 2016

    The Erratum to this article has been published in BMC Medical Genomics 2016 9:39

  18. Research article

    Comparison of two high-throughput semiconductor chip sequencing platforms in noninvasive prenatal testing for Down syndrome in early pregnancy

    Noninvasive prenatal testing (NIPT) to detect fetal aneuploidy using next-generation sequencing on ion semiconductor platforms has become common. There are several sequencers that can generate sufficient DNA r...

    Sunshin Kim, HeeJung Jung, Sung Hee Han, SeungJae Lee, JeongSub Kwon, Min Gyun Kim, Hyungsik Chu, Hongliang Chen, Kyudong Han, Hwanjong Kwak, Sunghoon Park, Hee Jae Joo, Byung Chul Kim and Jong Bhak

    BMC Medical Genomics 2016 9:22

    Published on: 30 April 2016

  19. Research article

    Longitudinal genome-wide methylation study of Roux-en-Y gastric bypass patients reveals novel CpG sites associated with essential hypertension

    Essential hypertension is a significant risk factor for cardiovascular diseases. Emerging research suggests a role of DNA methylation in blood pressure physiology. We aimed to investigate epigenetic associatio...

    Adrian E. Boström, Jessica Mwinyi, Sarah Voisin, Wenting Wu, Bernd Schultes, Kang Zhang and Helgi B. Schiöth

    BMC Medical Genomics 2016 9:20

    Published on: 22 April 2016

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