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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 or genetic disorders as well as the analysis of the structure and function of genes and chromosomes and the role of genetic mutations and cytogenetic changes in human genetic disorders.

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  1. Formalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nu...

    Authors: Jackie L. Ludgate, James Wright, Peter A. Stockwell, Ian M. Morison, Michael R. Eccles and Aniruddha Chatterjee

    Citation: BMC Medical Genomics 2017 10:54

    Content type: Technical advance

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  2. 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 ...

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

    Citation: BMC Medical Genomics 2017 10:49

    Content type: Case report

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  3. 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...

    Authors: 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…

    Citation: BMC Medical Genomics 2017 10:33

    Content type: Technical advance

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  4. 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...

    Authors: 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

    Citation: BMC Medical Genomics 2017 10:22

    Content type: Research article

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  5. 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...

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

    Citation: BMC Medical Genomics 2017 10:21

    Content type: Research article

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  6. Basal-like constitutes an important molecular subtype of breast cancer characterised by an aggressive behaviour and a limited therapy response. The outcome of patients within this subtype is, however, divergen...

    Authors: Heloisa H. Milioli, Inna Tishchenko, Carlos Riveros, Regina Berretta and Pablo Moscato

    Citation: BMC Medical Genomics 2017 10:19

    Content type: Research Article

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  7. 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...

    Authors: 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

    Citation: BMC Medical Genomics 2017 10:17

    Content type: Research article

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  8. 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...

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

    Citation: BMC Medical Genomics 2017 10:14

    Content type: Research article

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  9. 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...

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

    Citation: BMC Medical Genomics 2017 10:9

    Content type: Research article

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  10. 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...

    Authors: 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

    Citation: BMC Medical Genomics 2017 10:8

    Content type: Research article

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  11. 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...

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

    Citation: BMC Medical Genomics 2017 10:5

    Content type: Case report

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  12. 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 ...

    Authors: Andrew Smart, Deborah A. Bolnick and Richard Tutton

    Citation: BMC Medical Genomics 2017 10:3

    Content type: Debate

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  13. 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...

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

    Citation: BMC Medical Genomics 2016 9:65

    Content type: Technical advance

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  14. 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...

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

    Citation: BMC Medical Genomics 2016 9:62

    Content type: Correspondence

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  15. 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...

    Authors: 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

    Citation: BMC Medical Genomics 2016 9:58

    Content type: Research article

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  16. 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...

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

    Citation: BMC Medical Genomics 2016 9:54

    Content type: Research article

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  17. 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...

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

    Citation: BMC Medical Genomics 2016 9:40

    Content type: Research article

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  18. 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...

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

    Citation: BMC Medical Genomics 2016 9:26

    Content type: Research Article

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

  19. 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...

    Authors: 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

    Citation: BMC Medical Genomics 2016 9:22

    Content type: Research article

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  20. 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...

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

    Citation: BMC Medical Genomics 2016 9:20

    Content type: Research article

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  21. Liver cancer, of which hepatocellular carcinoma (HCC) is by far the most common type, is the second most deadly cancer (746,000 deaths in 2012). Currently, the only curative treatment for HCC is surgery to rem...

    Authors: Qing Yan Xie, Anthony Almudevar, Christa L. Whitney-Miller, Christopher T. Barry and Matthew N. McCall

    Citation: BMC Medical Genomics 2016 9:18

    Content type: Research article

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  22. Faced with an increasing number of choices for biologic therapies, rheumatologists have a critical need for better tools to inform rheumatoid arthritis (RA) disease management. The ability to identify patients...

    Authors: Ty M. Thomson, Reynald M. Lescarbeau, David A. Drubin, Daphna Laifenfeld, David de Graaf, David A. Fryburg, Bruce Littman, Renée Deehan and Aaron Van Hooser

    Citation: BMC Medical Genomics 2015 8:26

    Content type: Research article

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  23. Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the pr...

    Authors: Anna Kluska, Aneta Balabas, Agnieszka Paziewska, Maria Kulecka, Dorota Nowakowska, Michal Mikula and Jerzy Ostrowski

    Citation: BMC Medical Genomics 2015 8:19

    Content type: Research article

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  24. The gene expression profile of cytologically-normal bronchial airway epithelial cells has previously been shown to be altered in patients with lung cancer. Although bronchoscopy is often used for the diagnosis...

    Authors: Duncan H Whitney, Michael R Elashoff, Kate Porta-Smith, Adam C Gower, Anil Vachani, J Scott Ferguson, Gerard A Silvestri, Jerome S Brody, Marc E Lenburg and Avrum Spira

    Citation: BMC Medical Genomics 2015 8:18

    Content type: Research article

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  25. Early detection and treatment of non-invasive neoplasms can effectively reduce the incidence of advanced gastric carcinoma (GC), but only when the lineage is continuous between non-invasive and advanced tumour...

    Authors: Diem Thi-Ngoc Vo, Takahisa Nakayama, Hiroto Yamamoto, Ken-ichi Mukaisho, Takanori Hattori and Hiroyuki Sugihara

    Citation: BMC Medical Genomics 2015 8:6

    Content type: Research article

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  26. Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy numb...

    Authors: Joseph M Foster, Assa Oumie, Fiona S Togneri, Fabiana Ramos Vasques, Debra Hau, Morag Taylor, Emma Tinkler-Hundal, Katie Southward, Paul Medlow, Keith McGreeghan-Crosby, Iris Halfpenny, Dominic J McMullan, Phil Quirke, Katherine E Keating, Mike Griffiths, Karen G Spink…

    Citation: BMC Medical Genomics 2015 8:5

    Content type: Technical advance

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  27. Exacerbations of chronic obstructive pulmonary disease (COPD), characterized by acute deterioration in symptoms, may be due to bacterial or viral infections, environmental exposures, or unknown factors. Exacer...

    Authors: Jarrett D Morrow, Weiliang Qiu, Divya Chhabra, Stephen I Rennard, Paula Belloni, Anton Belousov, Sreekumar G Pillai and Craig P Hersh

    Citation: BMC Medical Genomics 2015 8:1

    Content type: Research article

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  28. Molecular karyotyping is now the first-tier genetic test for patients affected with unexplained intellectual disability (ID) and/or multiple congenital anomalies (MCA), since it identifies a pathogenic copy nu...

    Authors: Guylaine D’Amours, Mathieu Langlois, Géraldine Mathonnet, Raouf Fetni, Sonia Nizard, Myriam Srour, Frédérique Tihy, Michael S Phillips, Jacques L Michaud and Emmanuelle Lemyre

    Citation: BMC Medical Genomics 2014 7:70

    Content type: Research article

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  29. Neoadjuvant chemoradiotherapy (nCRT) followed by radical surgery is the preferred treatment strategy for locally advanced rectal cancer. However, complete tumor regression is observed in a significant proporti...

    Authors: Camila Miranda Lopes-Ramos, Angelita Habr-Gama, Bruna de Souza Quevedo, Natália Mariana Felício, Fabiana Bettoni, Fernanda Christtanini Koyama, Paula Fontes Asprino, Pedro Alexandre Galante, Joaquim Gama-Rodrigues, Anamaria Aranha Camargo, Rodrigo Oliva Perez and Raphael Bessa Parmigiani

    Citation: BMC Medical Genomics 2014 7:68

    Content type: Research article

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  30. In developing countries, many cases with rare neurological diseases remain undiagnosed due to limited diagnostic experience. We encountered a case in China where two siblings both began to develop idiopathic p...

    Authors: Lingling Shi, Bingxiao Li, Yonglan Huang, Xueying Ling, Tianyun Liu, Gholson J Lyon, Anding Xu and Kai Wang

    Citation: BMC Medical Genomics 2014 7:66

    Content type: Research article

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  31. We have identified candidate protein and microRNA (miRNA) biomarkers for dyspnea by studying serum, lavage fluid, and urine from military personnel who reported serious respiratory symptoms after they were dep...

    Authors: Joseph N Brown, Heather M Brewer, Carrie D Nicora, Karl K Weitz, Michael J Morris, Andrew J Skabelund, Joshua N Adkins, Richard D Smith, Ji-Hoon Cho and Richard Gelinas

    Citation: BMC Medical Genomics 2014 7:58

    Content type: Research article

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  32. Prediction models for old-age mortality have generally relied upon conventional markers such as plasma-based factors and biophysiological characteristics. However, it is unknown whether the existing markers ar...

    Authors: Juulia Jylhävä, Jani Raitanen, Saara Marttila, Antti Hervonen, Marja Jylhä and Mikko Hurme

    Citation: BMC Medical Genomics 2014 7:54

    Content type: Research article

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  33. MiRNA expression profiling is being actively investigated as a clinical biomarker and diagnostic tool to detect multiple cancer types and stages as well as other complex diseases. Initial investigations, howev...

    Authors: Renata A Rawlings-Goss, Michael C Campbell and Sarah A Tishkoff

    Citation: BMC Medical Genomics 2014 7:53

    Content type: Research article

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  34. Good prognostic tools for predicting disease progression in early stage prostate cancer (PCa) are still missing. Detection of molecular subtypes, for instance by using microarray gene technology, can give new ...

    Authors: Morten Beck Rye, Helena Bertilsson, Finn Drabløs, Anders Angelsen, Tone F Bathen and May-Britt Tessem

    Citation: BMC Medical Genomics 2014 7:50

    Content type: Research article

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  35. Recent advances in time-lapse monitoring in IVF treatment have provided new morphokinetic markers for embryonic competence. However, there is still very limited information about the relationship between morph...

    Authors: Zhihong Yang, John Zhang, Shala A Salem, Xiaohong Liu, Yanping Kuang, Rifaat D Salem and Jiaen Liu

    Citation: BMC Medical Genomics 2014 7:38

    Content type: Research article

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  36. Invasion of tumor cells into adjacent brain parenchyma is a major cause of treatment failure in glioblastoma. Furthermore, invasive tumors are shown to have a different genomic composition and metabolic abnorm...

    Authors: Rivka R Colen, Mark Vangel, Jixin Wang, David A Gutman, Scott N Hwang, Max Wintermark, Rajan Jain, Manal Jilwan-Nicolas, James Y Chen, Prashant Raghavan, Chad A Holder, Daniel Rubin, Eric Huang, Justin Kirby, John Freymann, Carl C Jaffe…

    Citation: BMC Medical Genomics 2014 7:30

    Content type: Research article

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  37. Widespread adoption of genomic technologies in the management of heterogeneous indications, including Multiple Myeloma, has been hindered by concern over variation between published gene expression signatures,...

    Authors: Ryan van Laar, Rachel Flinchum, Nathan Brown, Joseph Ramsey, Sam Riccitelli, Christoph Heuck, Bart Barlogie and John D Shaughnessy Jr

    Citation: BMC Medical Genomics 2014 7:25

    Content type: Technical advance

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  38. Fanconi anemia (FA) is a rare inherited genetic syndrome with highly variable clinical manifestations. Fifteen genetic subtypes of FA have been identified. Traditional complementation tests for grouping studie...

    Authors: Lixian Chang, Weiping Yuan, Huimin Zeng, Quanquan Zhou, Wei Wei, Jianfeng Zhou, Miaomiao Li, Xiaomin Wang, Mingjiang Xu, Fengchun Yang, Yungui Yang, Tao Cheng and Xiaofan Zhu

    Citation: BMC Medical Genomics 2014 7:24

    Content type: Research article

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  39. Clinical specimens undergoing diagnostic molecular pathology testing are fixed in formalin due to the necessity for detailed morphological assessment. However, formalin fixation can cause major issues with mol...

    Authors: Stephen Q Wong, Jason Li, Angela Y-C Tan, Ravikiran Vedururu, Jia-Min B Pang, Hongdo Do, Jason Ellul, Ken Doig, Anthony Bell, Grant A McArthur, Stephen B Fox, David M Thomas, Andrew Fellowes, John P Parisot and Alexander Dobrovic

    Citation: BMC Medical Genomics 2014 7:23

    Content type: Research article

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  40. Immediately after renal transplantation, patients experience rapid and significant improvement of their clinical conditions and undergo considerable systemic and cellular modifications. However, some patients ...

    Authors: Gianluigi Zaza, Federica Rascio, Paola Pontrelli, Simona Granata, Patrizia Stifanelli, Matteo Accetturo, Nicola Ancona, Loreto Gesualdo, Antonio Lupo and Giuseppe Grandaliano

    Citation: BMC Medical Genomics 2014 7:14

    Content type: Research article

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  41. Non-invasive prenatal testing of trisomy 21 (T21) is being actively investigated using fetal-specific epigenetic markers (EPs) that are present in maternal plasma. Recently, 12 EPs on chromosome 21 were identi...

    Authors: Ji Hyae Lim, Da Eun Lee, So Yeon Park, Do Jin Kim, Hyun Kyong Ahn, You Jung Han, Moon Young Kim and Hyun Mee Ryu

    Citation: BMC Medical Genomics 2014 7:1

    Content type: Research article

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  42. Myocardial infarction (MI) often results in left ventricular (LV) remodeling followed by heart failure (HF). It is of great clinical importance to understand the molecular mechanisms that trigger transition fr...

    Authors: Dorota Tulacz, Urszula Mackiewicz, Michal Maczewski, Agata Maciejak, Monika Gora and Beata Burzynska

    Citation: BMC Medical Genomics 2013 6:49

    Content type: Research article

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  43. Resilience or the ability of our body to cope with daily-life challenges has been proposed as a new definition of health, with restoration of homeostasis as target resultant of various physiological stress res...

    Authors: Suzan Wopereis, Danielle Wolvers, Marjan van Erk, Michiel Gribnau, Bas Kremer, Ferdi A van Dorsten, Esther Boelsma, Ursula Garczarek, Nicole Cnubben, Leon Frenken, Paul van der Logt, Henk FJ Hendriks, Ruud Albers, John van Duynhoven, Ben van Ommen and Doris M Jacobs

    Citation: BMC Medical Genomics 2013 6:44

    Content type: Research article

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  44. Tumour growth in colorectal cancer and other solid cancers is frequently supported by activating mutations in the epidermal growth factor receptor (EGFR) signaling pathway (Patholog Res Int 2011:932932, 2011)....

    Authors: Samuel Wormald, Liz Milla and Liam O’Connor

    Citation: BMC Medical Genomics 2013 6:43

    Content type: Research article

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  45. Bladder cancer exists as several distinct subtypes, including urothelial carcinoma (UCa), squamous cell carcinoma (SCCa), adenocarcinoma and small cell carcinoma. These entities, despite showing distinct morph...

    Authors: Donna E Hansel, Zhongfa Zhang, David Petillo and Bin T Teh

    Citation: BMC Medical Genomics 2013 6:42

    Content type: Research article

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  46. The majority of gastric cancer cases are believed to be caused by chronic infection with the bacterium Helicobacter pylori, and atrophic corpus gastritis is a predisposing condition to gastric cancer development....

    Authors: Intawat Nookaew, Kaisa Thorell, Kuntal Worah, Shugui Wang, Martin Lloyd Hibberd, Henrik Sjövall, Sven Pettersson, Jens Nielsen and Samuel B Lundin

    Citation: BMC Medical Genomics 2013 6:41

    Content type: Research article

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Announcement

As a result of the significant disruption that is being caused by the COVID-19 pandemic we are very aware that many researchers will have difficulty in meeting the timelines associated with our peer review process during normal times.  Please do let us know if you need additional time. Our systems will continue to remind you of the original timelines but we intend to be highly flexible at this time.