Genome Medicine Journal Impact Factor & Information

Publisher: BioMed Central

Journal description

Current impact factor: 4.94

Impact Factor Rankings

2015 Impact Factor Available summer 2015
2013 / 2014 Impact Factor 4.942
2012 Impact Factor 3.397

Additional details

5-year impact 3.54
Cited half-life 2.70
Immediacy index 0.71
Eigenfactor 0.01
Article influence 1.50
ISSN 1756-994X

Publisher details

BioMed Central

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Publisher's version/PDF may be used
    • Eligible UK authors may deposit in OpenDepot
    • Creative Commons Attribution License
    • Copy of License must accompany any deposit.
    • All titles are open access journals
    • 'BioMed Central' is an imprint of 'Springer Verlag (Germany)'
  • Classification
    ‚Äč green

Publications in this journal

  • Genome Medicine 12/2015; 7(1). DOI:10.1186/s13073-015-0170-2
  • Genome Medicine 12/2015; 7(1). DOI:10.1186/s13073-015-0171-1
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    ABSTRACT: Three-dimensional organotypic culture models show great promise as a tool for cancer precision medicine, with potential applications for oncogene modeling, gene discovery and chemosensitivity studies.
    Genome Medicine 12/2015; 7(1):32. DOI:10.1186/s13073-015-0158-y
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    ABSTRACT: Regenerative medicine has a three-body problem: alignment of the dynamics of the genome, stem cell and patient. Focusing on the rare inherited fragile skin disorder epidermolysis bullosa, three recent innovative studies have used induced pluripotent stem cells and gene correction, revertant mosaicism or genome editing to advance the prospects of better cell-based therapeutics to restore skin structure and function for epidermolysis bullosa and potentially other inherited diseases.
    Genome Medicine 12/2015; 7(1):15. DOI:10.1186/s13073-015-0141-7
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    ABSTRACT: Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution and resulting polymorphisms, which prevent reads from aligning readily to commonly used virus reference genomes, and, accordingly, make virus integration sites difficult to detect. Another confounding factor is host genomic instability as a result of virus insertions. To tackle these challenges and improve our capability to identify cryptic virus-host fusions, we present a new approach that detects Virus intEgration sites through iterative Reference SEquence customization (VERSE). To the best of our knowledge, VERSE is the first approach to improve detection through customizing reference genomes. Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection. VERSE is implemented in the open source package VirusFinder 2 that is available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
    Genome Medicine 12/2015; 7(1):2. DOI:10.1186/s13073-015-0126-6
  • Genome Medicine 12/2015; 7(1). DOI:10.1186/s13073-015-0169-8
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    ABSTRACT: Recent work has linked specific genetic variation found in human populations to risk for developing neuropsychiatric diseases. How that risk is mediated through molecular-, cellular- and systems-level mechanisms now becomes the central question in this field. Two recent papers studying high-penetrance copy number variation at chromosome 16p11.2 find large changes in brain structure, refining hypotheses about the regions of the brain that are affected and implicating specific neurodevelopmental processes in these changes.
    Genome Medicine 12/2015; 7(1):13. DOI:10.1186/s13073-015-0140-8
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    ABSTRACT: Variant interpretation is a central challenge in genomic medicine. A recent study demonstrates the power of Bayesian statistical approaches to improve interpretation of variants in the context of specific genes and syndromes. Such Bayesian approaches combine frequency (in the form of observed genetic variation in cases and controls) with biological annotations to determine a probability of pathogenicity. These Bayesian approaches complement other efforts to catalog human variation. See related Research; 10.1186/s13073-014-0120-4.
    Genome Medicine 12/2015; 7(1):4. DOI:10.1186/s13073-015-0129-3
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    ABSTRACT: Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (<36 h) required for fresh embryo transfer. Here, we describe and validate a method for inferring the inherited whole genome sequence of an embryo for preimplantation genetic diagnosis (PGD). We combine haplotype-resolved, parental genome sequencing with rapid embryo genotyping to predict the whole genome sequence of a day-5 human embryo in a couple at risk of transmitting alpha-thalassemia. Inheritance was predicted at approximately 3 million paternally and/or maternally heterozygous sites with greater than 99% accuracy. Furthermore, we successfully phase and predict the transmission of an HBA1/HBA2 deletion from each parent. Our results suggest that preimplantation whole genome prediction may facilitate the comprehensive diagnosis of diseases with a known genetic basis in embryos.
    Genome Medicine 12/2015; 7(1). DOI:10.1186/s13073-015-0160-4
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    ABSTRACT: Aristolochic acid (AA) is a natural compound found in many plants of the Aristolochia genus, and these plants are widely used in traditional medicines for numerous conditions and for weight loss. Previous work has connected AA-mutagenesis to upper-tract urothelial cell carcinomas and hepatocellular carcinomas. We hypothesize that AA may also contribute to bladder cancer. Here, we investigated the involvement of AA-mutagenesis in bladder cancer by sequencing bladder tumor genomes from two patients with known exposure to AA. After detecting strong mutational signatures of AA exposure in these tumors, we exome-sequenced and analyzed an additional 11 bladder tumors and analyzed publicly available somatic mutation data from a further 336 bladder tumors. The somatic mutations in the bladder tumors from the two patients with known AA exposure showed overwhelming AA signatures. We also detected evidence of AA exposure in 1 out of 11 bladder tumors from Singapore and in 3 out of 99 bladder tumors from China. In addition, 1 out of 194 bladder tumors from North America showed a pattern of mutations that might have resulted from exposure to an unknown mutagen with a heretofore undescribed pattern of A > T mutations. Besides the signature of AA exposure, the bladder tumors also showed the CpG > TpG and activated-APOBEC signatures, which have been previously reported in bladder cancer. This study demonstrates the utility of inferring mutagenic exposures from somatic mutation spectra. Moreover, AA exposure in bladder cancer appears to be more pervasive in the East, where traditional herbal medicine is more widely used. More broadly, our results suggest that AA exposure is more extensive than previously thought both in terms of populations at risk and in terms of types of cancers involved. This appears to be an important public health issue that should be addressed by further investigation and by primary prevention through regulation and education. In addition to opportunities for primary prevention, knowledge of AA exposure would provide opportunities for secondary prevention in the form of intensified screening of patients with known or suspected AA exposure.
    Genome Medicine 12/2015; 7(1). DOI:10.1186/s13073-015-0161-3
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    ABSTRACT: Somatic mutations affecting components of the RNA splicing machinery occur with high frequencies across many tumor types. These mutations give rise to distinct alterations in normal splice site and exon recognition, such as unusual 3' splice site preferences, that likely contribute to tumorigenesis. We analyzed genome-wide patterns of RNA splicing across 805 matched tumor and normal control samples from 16 distinct cancer types to identify signals of abnormal cancer-associated splicing. We found that abnormal RNA splicing, typified by widespread intron retention, is common across cancers even in the absence of mutations directly affecting the RNA splicing machinery. Almost all liquid and solid cancer types exhibited frequent retention of both alternative and constitutive introns relative to control normal tissues. The sole exception was breast cancer, where intron retention typified adjacent normal rather than cancer tissue. Different introns were preferentially retained in specific cancer types, although a small subset of introns enriched for genes encoding RNA splicing and export factors exhibited frequent retention across diverse cancers. The extent of intron retention correlated with the presence of IDH1 and IDH2 mutations in acute myeloid leukemia and across molecular subtypes in breast cancer. Many introns that were preferentially retained in primary cancers were present at high levels in the cytoplasmic mRNA pools of cancer cell lines. Our data indicate that abnormal RNA splicing is a common characteristic of cancers even in the absence of mutational insults to the splicing machinery, and suggest that intron-containing mRNAs contribute to the transcriptional diversity of many cancers.
    Genome Medicine 12/2015; 7(1). DOI:10.1186/s13073-015-0168-9