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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. Pancreatic cancer is one of the most common malignant tumors of the digestive tract, and it has a poor prognosis. Traditional methods are not effective to accurately assess the prognosis of patients with pancr...

    Authors: Wenting Wang, Zhijian Xu, Ning Wang, Ruyong Yao, Tao Qin, Hao Lin and Lu Yue

    Citation: BMC Medical Genomics 2021 14:42

    Content type: Research article

    Published on:

  2. Acute myeloid leukemia (AML) is biologically heterogeneous diseases with adverse prognosis. This study was conducted to find prognostic biomarkers that could effectively classify AML patients and provide guida...

    Authors: Yanli Lai, Guifang OuYang, Lixia Sheng, Yanli Zhang, Binbin Lai and Miao Zhou

    Citation: BMC Medical Genomics 2021 14:39

    Content type: Research article

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  3. Mutations in the PRKAG2 gene encoding the 5′ Adenosine Monophosphate-Activated Protein Kinase (AMPK), specifically in its γ2 regulatory subunit, lead to Glycogen storage disease of heart, fetal congenital diso...

    Authors: Zahra Beyzaei, Fatih Ezgu, Bita Geramizadeh, Alireza Alborzi and Alireza Shojazadeh

    Citation: BMC Medical Genomics 2021 14:33

    Content type: Case report

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  5. Peripheral immune response has been revealed to play a critical role in proliferative vitreoretinopathy (PVR). However, the reliable immune-related factors that are acting as prognostic indicators or therapeut...

    Authors: Yao Ni, Fangyuan Liu, Xiao Hu, Yingyan Qin and Zhaotian Zhang

    Citation: BMC Medical Genomics 2021 14:30

    Content type: Research article

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  6. Mutations in lysyl-tRNA synthetase (KARS1), an enzyme that charges tRNA with the amino acid lysine in both the cytoplasm and mitochondria, have been associated thus far with autosomal recessive Charcot–Marie–Toot...

    Authors: Francesca Peluso, Viviana Palazzo, Giuseppe Indolfi, Francesco Mari, Roberta Pasqualetti, Elena Procopio, Claudia Nesti, Renzo Guerrini, Filippo Santorelli and Sabrina Giglio

    Citation: BMC Medical Genomics 2021 14:25

    Content type: Case report

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  7. Previous studies have revealed that mutations of Spalt Like Transcription Factor 1 (SALL1) are responsible for Townes-Brocks syndrome (TBS), a rare genetic disorder that is characterized by an imperforate anus, d...

    Authors: Guangxian Yang, Yi Yin, Zhiping Tan, Jian Liu, Xicheng Deng and Yifeng Yang

    Citation: BMC Medical Genomics 2021 14:24

    Content type: Research article

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  8. Pure red cell aplasia (PRCA) and large granular lymphocytic leukaemia (LGLL) are very rare complications of autoimmune polyendocrine syndrome type 1 (APS1). Here, we report a case of APS1 with PRCA and LGLL. P...

    Authors: Jing Ruan, Xuan Wang, Xianyong Jiang and Miao Chen

    Citation: BMC Medical Genomics 2021 14:22

    Content type: Case report

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  9. To make the right treatment decisions about colorectal cancer (CRC) patients reliable predictive and prognostic data are needed. However, in many cases this data is not enough. Some studies suggest that LRIG1 gen...

    Authors: Maryam Bakherad, Mahdieh Salimi, Seyed Abdolhamid Angaji, Frouzandeh Mahjoubi and Tayebeh Majidizadeh

    Citation: BMC Medical Genomics 2021 14:20

    Content type: Research article

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  10. Some ultrasonic soft markers can be found during ultrasound examination. However, the etiology of the fetuses with ultrasonic soft markers is still unknown. This study aimed to evaluate the genetic etiology an...

    Authors: Meiying Cai, Na Lin, Xuemei Chen, Meimei Fu, Nan Guo, Liangpu Xu and Hailong Huang

    Citation: BMC Medical Genomics 2021 14:19

    Content type: Research article

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  12. Familial progressive hyper- and hypopigmentation (FPHH, MIM 145250) is a rare hereditary skin disorder that is predominantly characterized by progressive, diffuse, partly blotchy hyperpigmented lesions intermi...

    Authors: Jianbo Wang, Weisheng Li, Naihui Zhou, Jingliu Liu, Shoumin Zhang, Xueli Li, Zhenlu Li, Ziliang Yang, Miao Sun and Min Li

    Citation: BMC Medical Genomics 2021 14:12

    Content type: Research article

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  13. Corneal dystrophies (CDs) are a heterogeneous group of bilateral, genetically determined, noninflammatory bilateral corneal diseases that are usually limited to the cornea. CD is characterized by a large varia...

    Authors: Yahya Benbouchta, Imane Cherkaoui Jaouad, Habiba Tazi, Hamza Elorch, Mouna Ouhenach, Abdelali Zrhidri, Khalid Sadki, Abdelaziz Sefiani, Jaber Lyahyai and Amina Berraho

    Citation: BMC Medical Genomics 2021 14:9

    Content type: Case report

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  14. The abnormal expression of activating transcription factor 3 (ATF3), a member of the basic leucine zipper (bZIP) family of transcription factors, is associated with carcinogenesis. However, the expression patt...

    Authors: Lijuan Li, Shaohua Song, Xiaoling Fang and Donglin Cao

    Citation: BMC Medical Genomics 2021 14:8

    Content type: Research article

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  15. In addition to ovarian and breast cancers, loss-of-function mutations in BRCA1 and BRCA2 genes are also linked to an increased risk of pancreatic cancer, with ~ 4 to 7% of pancreatic cancer patients harboring ger...

    Authors: Deqiang Wang, Ruting Guan, Qing Tao, Sisi Liu, Man Yu and Xiaoqin Li

    Citation: BMC Medical Genomics 2021 14:6

    Content type: Case report

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  16. Hearing loss/deafness is a common otological disorder found in the Pakistani population due to the high prevalence of consanguineous unions, but the full range of genetic causes is still unknown.

    Authors: Ashfaque Ahmed, Meng Wang, Rizwan Khan, Abid Ali Shah, Hui Guo, Sajid Malik, Kun Xia and Zhengmao Hu

    Citation: BMC Medical Genomics 2021 14:2

    Content type: Research article

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  17. Variants in CDKN2B/CDKN2B-AS1 have been reported to modulate glaucoma risk in several GWAS across different populations. CDKN2B/CDKN2A encodes tumor suppressor proteins p16INK4A/p15INK4B which influences cell pro...

    Authors: Nanamika Thakur, Manu Kupani, Rashim Mannan, Archna Pruthi and Sanjana Mehrotra

    Citation: BMC Medical Genomics 2021 14:1

    Content type: Research article

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  20. Mutations in CNKSR2 have been described in patients with neurodevelopmental disorders characterized by childhood epilepsy, language deficits, and attention problems. The encoded protein plays an important role in...

    Authors: Yi Zhang, Tingting Yu, Niu Li, Jiwen Wang, Jian Wang, Yihua Ge and Ruen Yao

    Citation: BMC Medical Genomics 2020 13:182

    Content type: Case report

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  21. The Cancer Genome Atlas identified four molecular subgroups of endometrial cancer with survival differences based on whole genome, transcriptomic, and proteomic characterization. Clinically accessible algorith...

    Authors: Eirwen M. Miller, Nicole E. Patterson, Gregory M. Gressel, Rouzan G. Karabakhtsian, Michal Bejerano-Sagie, Nivedita Ravi, Alexander Maslov, Wilber Quispe-Tintaya, Tao Wang, Juan Lin, Harriet O. Smith, Gary L. Goldberg, Dennis Y. S. Kuo and Cristina Montagna

    Citation: BMC Medical Genomics 2020 13:179

    Content type: Research article

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  22. Biomarker identification is one of the major and important goal of functional genomics and translational medicine studies. Large scale –omics data are increasingly being accumulated and can provide vital means...

    Authors: Animesh Acharjee, Joseph Larkman, Yuanwei Xu, Victor Roth Cardoso and Georgios V. Gkoutos

    Citation: BMC Medical Genomics 2020 13:178

    Content type: Research article

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  23. Colorectal cancer (CRC) is a multifactorial tumor and a leading cause of cancer-specific deaths worldwide. Recent research has shown that the alteration of intestinal flora contributes to the development of CR...

    Authors: Jiayu Zhang, Huaiyu Zhang, Faping Li, Zheyu Song, Yezhou Li and Tiancheng Zhao

    Citation: BMC Medical Genomics 2020 13:172

    Content type: Research article

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  24. MYCN amplification is the most important genomic feature in neuroblastoma (NB). However, limited studies have been conducted on the MYCN non-amplified NB including low- and intermediate-risk NB. Here, the genomic...

    Authors: Eunjin Lee, Ji Won Lee, Boram Lee, Kyunghee Park, Joonho Shim, Keon Hee Yoo, Hong Hoe Koo, Ki Woong Sung and Woong-Yang Park

    Citation: BMC Medical Genomics 2020 13:171

    Content type: Research article

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  25. ‘Precision oncology’ can ensure the best suitable treatment at the right time by tailoring treatment towards individual patient and comprehensive tumour characteristics. In current molecular pathology, diagnos...

    Authors: Kris G. Samsom, Linda J. W. Bosch, Luuk J. Schipper, Paul Roepman, Ewart de Bruijn, Louisa R. Hoes, Immy Riethorst, Lieke Schoenmaker, Lizet E. van der Kolk, Valesca P. Retèl, Geert W. J. Frederix, Tineke E. Buffart, Jacobus J. M. van der Hoeven, Emile E. Voest, Edwin Cuppen, Kim Monkhorst…

    Citation: BMC Medical Genomics 2020 13:169

    Content type: Study protocol

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  26. Complex genomic changes that arise in tumors are a consequence of chromosomal instability. In tumor cells genomic aberrations disrupt core signaling pathways involving various genes, thus delineating of signal...

    Authors: Akeen Kour, Vasudha Sambyal, Kamlesh Guleria, Neeti Rajan Singh, Manjit Singh Uppal, Mridu Manjari and Meena Sudan

    Citation: BMC Medical Genomics 2020 13:168

    Content type: Research article

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  27. NEK2 has an established involvement in hepatocellular carcinoma (HCC) but the roles of NEK2 and its interacting proteins in HCC have not been systematically explored.

    Authors: Lu Zeng, Xiude Fan, Xiaoyun Wang, Huan Deng, Xiaoge Zhang, Kun Zhang, Shan He, Na Li, Qunying Han and Zhengwen Liu

    Citation: BMC Medical Genomics 2020 13:158

    Content type: Research article

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  28. The use of noninvasive techniques to determine paternity prenatally is increasing because it reduces the risks associated with invasive procedures. Current methods, based on SNPs, use the analysis of at least ...

    Authors: Jaqueline Yu Ting Wang, Martin R. Whittle, Renato David Puga, Anatoly Yambartsev, André Fujita and Helder I. Nakaya

    Citation: BMC Medical Genomics 2020 13:157

    Content type: Technical advance

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  29. Treating cancer depends in part on identifying the mutations driving each patient’s disease. Many clinical laboratories are adopting high-throughput sequencing for assaying patients’ tumours, applying targeted...

    Authors: Ali Karimnezhad, Gareth A. Palidwor, Kednapa Thavorn, David J. Stewart, Pearl A. Campbell, Bryan Lo and Theodore J. Perkins

    Citation: BMC Medical Genomics 2020 13:156

    Content type: Research article

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  30. Identification of master regulators (MRs) using transcriptome data in cervical cancer (CC) could help us to develop biomarkers and find novel drug targets to fight this disease.

    Authors: Beiwei Yu, Long Chen, Weina Zhang, Yue Li, Yibiao Zhang, Yuan Gao, Xianlin Teng, Libo Zou, Qian Wang, Hongtao Jia, Xiangtao Liu, Hui Zheng, Ping Hou, Hongyan Yu, Ying Sun, Zhiqin Zhang…

    Citation: BMC Medical Genomics 2020 13:145

    Content type: Research article

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  31. Detection of somatic mutations in tumor tissues helps to understand tumor biology and guide treatment selection. Methods such as quantitative PCR can analyze a few mutations with high efficiency, while next ge...

    Authors: Chang Xu, Danli Peng, Jialu Li, Meihua Chen, Yujie Hu, Mingliang Hou, Qingjuan Shang, Qi Liang, Jie Li, Wenfeng Li, Xiaoli Wu, Changbao Liu, Wanle Hu, Mao Cai, Huxiang Zhang, Guorong Chen…

    Citation: BMC Medical Genomics 2020 13:143

    Content type: Research article

    Published on:

  32. A plethora of cases are reported in the literature with iso- and ring-chromosome 18. However, co-occurrence of these two abnormalities in an individual along with a third cell line and absence of numerical ano...

    Authors: Harsh Sheth, Sunil Trivedi, Thomas Liehr, Ketan Patel, Deepika Jain, Jayesh Sheth and Frenny Sheth

    Citation: BMC Medical Genomics 2020 13:141

    Content type: Case report

    Published on:

  33. Electronic cigarettes (e-cigs) vaping, cigarette smoke, and waterpipe tobacco smoking are associated with various cardiopulmonary diseases. microRNAs are present in higher concentration in exosomes that play a...

    Authors: Kameshwar P. Singh, Krishna P. Maremanda, Dongmei Li and Irfan Rahman

    Citation: BMC Medical Genomics 2020 13:128

    Content type: Research article

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  34. In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes. Typically, hapl...

    Authors: Qing Li, Yan Mao, Shaoying Li, Hongzi Du, Wenzhi He, Jianchun He, Lingyin Kong, Jun Zhang, Bo Liang and Jianqiao Liu

    Citation: BMC Medical Genomics 2020 13:117

    Content type: Technical advance

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  35. Congenital insensitivity to pain with anhidrosis (CIPA) is an extremely rare autosomal recessive disorder characterized by insensitivity to pain, inability to sweat and intellectual disability. CIPA is caused ...

    Authors: Andrés López-Cortés, Ana Karina Zambrano, Patricia Guevara-Ramírez, Byron Albuja Echeverría, Santiago Guerrero, Eliana Cabascango, Andy Pérez-Villa, Isaac Armendáriz-Castillo, Jennyfer M. García-Cárdenas, Verónica Yumiceba, Gabriela Pérez-M, Paola E. Leone and César Paz-y-Miño

    Citation: BMC Medical Genomics 2020 13:113

    Content type: Case report

    Published on:

  36. Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the ...

    Authors: Rong Wei, Ziyue Wang, Yaping Zhang, Bin Wang, Ningning Shen, Li E, Xin Li, Lifang Shang, Yangwei Shang, Wenpeng Yan, Xiaoqin Zhang, Wenxia Ma and Chen Wang

    Citation: BMC Medical Genomics 2020 13:112

    Content type: Research article

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  37. Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high sp...

    Authors: Stefanie Friedrich and Erik L. L. Sonnhammer

    Citation: BMC Medical Genomics 2020 13:110

    Content type: Technical advance

    Published on:

  38. The goal of this study was to determine whether Levey-Jennings charts, which are widely used in clinical laboratories, can be used to create standardized internal quality controls (IQCs) for prenatal molecular...

    Authors: Binghuan Weng, Ya-li Xu, Jun Ying, Hao-kun Yang, Lan Su, Yan-mei Yang and Min Chen

    Citation: BMC Medical Genomics 2020 13:109

    Content type: Research article

    Published on:

  39. Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exa...

    Authors: Arash Poursheikhani, Mohammad Reza Abbaszadegan, Negin Nokhandani and Mohammad Amin Kerachian

    Citation: BMC Medical Genomics 2020 13:108

    Content type: Research article

    Published on:

  40. We have evaluated an NGS-based method to detect recurrent gene fusions of diagnostic and prognostic importance in hematological malignancies. Our goal was to achieve a highly specific assay with a simple workf...

    Authors: Marie Engvall, Nicola Cahill, Britt-Inger Jonsson, Martin Höglund, Helene Hallböök and Lucia Cavelier

    Citation: BMC Medical Genomics 2020 13:106

    Content type: Research article

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  41. Liquid-based cytology (LBC) is now a widely used method for cytologic screening and cancer diagnosis. Since the cells are fixed with alcohol-based fixatives, and the specimens are stored in a liquid condition,...

    Authors: Toshiaki Akahane, Ikumi Kitazono, Shintaro Yanazume, Masaki Kamio, Shinichi Togami, Ippei Sakamoto, Sachio Nohara, Seiya Yokoyama, Hiroaki Kobayashi, Tsubasa Hiraki, Shinsuke Suzuki, Shinichi Ueno and Akihide Tanimoto

    Citation: BMC Medical Genomics 2020 13:101

    Content type: Research article

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  42. Non-invasive prenatal testing (NIPT) has been established as a routine prenatal screening to assess the risk of common foetal aneuploidy disorder (trisomy 21, 18, and 13). NIPT has high sensitivity and high sp...

    Authors: Hui-Hui Xu, Mei-Zhen Dai, Kai Wang, Yang Zhang, Fei-Yan Pan and Wei-Wu Shi

    Citation: BMC Medical Genomics 2020 13:96

    Content type: Case report

    Published on:

  43. Left-sided heart failure (HF) is documented as a key prognostic factor in HF. However, the relative molecular mechanisms underlying left-sided HF is unknown. The purpose of this study is to unearth significant...

    Authors: Jiamin Zhou, Wei Zhang, Chunying Wei, Zhiliang Zhang, Dasong Yi, Xiaoping Peng, Jingtian Peng, Ran Yin, Zeqi Zheng, Hongmei Qi, Yunfeng Wei and Tong Wen

    Citation: BMC Medical Genomics 2020 13:93

    Content type: Research article

    Published on:

  44. Medulloblastoma (MB) is one of the most common malignant cancers in children. MB is primarily classified into four subgroups based on molecular and clinical characteristics as (1) WNT (2) Sonic-hedgehog (SHH) ...

    Authors: Varun Kesherwani, Mamta Shukla, Don W. Coulter, J. Graham Sharp, Shantaram S. Joshi and Nagendra K. Chaturvedi

    Citation: BMC Medical Genomics 2020 13:87

    Content type: Research article

    Published on:

  45. A growing evidence suggests that long non-coding RNAs (lncRNAs) can function as a microRNA (miRNA) sponge in various diseases including oral cancer. However, the pathophysiological function of lncRNAs remains ...

    Authors: Junhao Yin, Xiaoli Zeng, Zexin Ai, Miao Yu, Yang’ou Wu and Shengjiao Li

    Citation: BMC Medical Genomics 2020 13:84

    Content type: Research article

    Published on:

  46. Intellectual disability (ID) is a heterogeneous neurodevelopmental disorder with a complex genetic underpinning in its etiology. Chromosome microarray (CMA) is recommended as the first-tier diagnostic test for...

    Authors: Jun Wang, Yan Wang, Liwen Wang, Wang Yang Chen and Min Sheng

    Citation: BMC Medical Genomics 2020 13:70

    Content type: Research article

    Published on:

  47. Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote ex...

    Authors: Chun-Lin Lin, Xi Tan, Meizhen Chen, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ya-Ting Hsu, Chiou-Miin Wang, Nameer Kirma, Chun-Liang Chen, Ching-Hung Lin, Kate I. Lathrop, Richard Elledge, Virginia G. Kaklamani, Kohzoh Mitsuya and Tim H.-M. Huang

    Citation: BMC Medical Genomics 2020 13:69

    Content type: Research article

    Published on:

  48. The causes for thousands of individually rare recessive diseases have been discovered since the adoption of next generation sequencing (NGS). Following the molecular diagnosis in older children in a family, pa...

    Authors: Mahmoud Y. Issa, Zinayida Chechlacz, Valentina Stanley, Renee D. George, Jennifer McEvoy-Venneri, Denice Belandres, Hasnaa M. Elbendary, Khaled R. Gaber, Ahmed Nabil, Mohamed S. Abdel-Hamid, Maha S. Zaki and Joseph G. Gleeson

    Citation: BMC Medical Genomics 2020 13:68

    Content type: Research article

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  49. Despite the emergence of cell-free DNA (cfDNA) as a clinical biomarker in cancer, the tissue origins of cfDNA in healthy individuals have to date been inferred only by indirect and relative measurement methods...

    Authors: Danny Laurent, Fiona Semple, Philip J. Starkey Lewis, Elaine Rose, Holly A. Black, Jennifer Coe, Stuart J. Forbes, Mark J. Arends, James W. Dear and Timothy J. Aitman

    Citation: BMC Medical Genomics 2020 13:60

    Content type: Research article

    Published on:

  50. The use of high-throughput analytical techniques has enabled the description of acute lymphoblastic leukaemia (ALL) subtypes. The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with...

    Authors: Monika Lejman, Monika Włodarczyk, Joanna Zawitkowska and Jerzy R. Kowalczyk

    Citation: BMC Medical Genomics 2020 13:58

    Content type: Case report

    Published on:

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