A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases.

Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.

Importance of Participant-Centricity and Trust for a Sustainable Medical Information Commons.

Drawing on a landscape analysis of existing data-sharing initiatives, in-depth interviews with expert stakeholders, and public deliberations with community advisory panels across the U.S., we describe features of the evolving medical information commons (MIC). We identify participant-centricity and trustworthiness as the most important features of an MIC and discuss the implications for those seeking to create a sustainable, useful, and widely available collection of linked resources for research and other purposes.

Next-generation sequencing for cancer drug development: the present and visions for the future.

NGS for Cancer Drug Development 24-26 September 2013, Boston, MA, USA Many of us who, prior to the -omics revolution, staunchly pursued the molecular basis of disease causation recognized the fundamental importance that biomarkers held for the eventuality of personalized medicine, more accurate diagnostics and targeted drug discovery. With slab sequencing apparatuses now mere memories relegated to the dusty reaches of old laboratory cabinets, we are fervently unraveling the complexities of many diseases through newer, more powerful innovative technologies. Quicker than ever before, we are achieving a deeper understanding of causative genetic lesions, perturbed pathways and the functions of altered networks. This has opened the door to a golden age of data generation that shows promise as a vital key to the successful treatment of human diseases. Hanson Wade recently organized a series of three related symposia that highlighted advances in industry and academic research in the areas of drug development, companion diagnostics and disease profiling: 'NGS for Cancer Drug Development' conference in Boston on 24-26 September 2013, the 'NGS Data Analysis' conference in San Francisco on 15-17 October 2013 and the 'World CDx' conference in Boston on 12-15 November 2013. These meetings provided forums for leaders to present advancements in personalized medicine, strategies for drug development, and innovations in diagnostics and other important areas. Their highly interactive nature also provided opportunities for industry and academic attendees to identify common hurdles that stand in the way of progress, (e.g., biomarker validation, analytical software limitations, data sharing, sample handling, regulatory and reimbursement restrictions), and to propose strategies for independent and community approaches toward overcoming such hurdles. In the interest of space, this review will be limited to the first in this series, the NGS for Cancer Drug Development conference, and its six major areas of focus.

On the future of genomic data.

Many of the challenges in genomics derive from the informatics needed to store and analyze the raw sequencing data that is available from highly multiplexed sequencing technologies. Because single week-long sequencing runs today can produce as much data as did entire genome centers a few years ago, the need to process terabytes of information has become de rigueur for many labs engaged in genomic research. The availability of deep (and large) genomic data sets raises concerns over information access, data security, and subject/patient privacy that must be addressed for the field to continue its rapid advances.

Interactions of sex hormone-binding globulin with target cells.

Sex hormone-binding globulin (SHBG) was initially described as a plasma protein synthesized in, and secreted by, the liver. It was discovered by its ability to bind certain androgens and estrogens and, for many years, was believed to serve as a transporter/reservoir for the steroids which it bound. Subsequently, it became clear that the cell membranes of selected tissues contained a receptor for SHBG (R(SHBG)). This review deals with what is known of that receptor - its anatomy, physiology and biochemistry.

Human sex hormone-binding globulin gene expression- multiple promoters and complex alternative splicing.

BACKGROUND: Human sex hormone-binding globulin (SHBG) regulates free sex steroid concentrations in plasma and modulates rapid, membrane based steroid signaling. SHBG is encoded by an eight exon-long transcript whose expression is regulated by a downstream promoter (P(L)). The SHBG gene was previously shown to express a second major transcript of unknown function, derived from an upstream promoter (P(T)), and two minor transcripts. RESULTS: We report that transcriptional expression of the human SHBG gene is far more complex than previously described. P(L) and P(T) direct the expression of at least six independent transcripts each, resulting from alternative splicing of exons 4, 5, 6, and/or 7. We mapped two transcriptional start sites downstream of P(L) and P(T), and present evidence for a third SHBG gene promoter (P(N)) within the neighboring FXR2 gene; PN regulates the expression of at least seven independent SHBG gene transcripts, each possessing a novel, 164-nt first exon (1N). Transcriptional expression patterns were generated for human prostate, breast, testis, liver, and brain, and the LNCaP, MCF-7, and HepG2 cell lines. Each expresses the SHBG transcript, albeit in varying abundance. Alternative splicing was more pronounced in the cancer cell lines. P(L)- P(T)- and P(N)-derived transcripts were most abundant in liver, testis, and prostate, respectively. Initial findings reveal the existence of a smaller immunoreactive SHBG species in LNCaP, MCF-7, and HepG2 cells. CONCLUSION: These results extend our understanding of human SHBG gene transcription, and raise new and important questions regarding the role of novel alternatively spliced transcripts, their function in hormonally responsive tissues including the breast and prostate, and the role that aberrant SHBG gene expression may play in cancer.

Sex hormone-binding globulin influences gene expression of LNCaP and MCF-7 cells in response to androgen and estrogen treatment.

Sex hormone-binding globulin (SHBG), a plasma protein that binds androgens and estrogens, also participates in the initial steps of a membrane-based steroid signaling pathway in human prostate and breast. We have recently shown that SHBG is expressed at the mRNA and protein levels in the prostate and breast. In this study, we addressed whether locally expressed SHBG: (1) Functions to regulate activation of membrane-based steroid signaling and (2) influences activation of the androgen (AR) and estrogen (ER) receptors. Using microarray analysis, we identified specific genes that are influenced by SHBG expression in LNCaP and MCF-7 cells in a manner consistent with each of these properties. These findings suggest that locally expressed SHBG can play a functional role in the steroid responsiveness of prostate and breast cells through multiple signaling pathways and that perturbations in local SHBG expression could contribute to prostate and breast cancer.

Assessment of putative protein targets derived from the SARS genome.

The ability to rapidly and reliably develop hypotheses on the function of newly discovered protein sequences requires systematic and comprehensive analysis. Such an analysis, embodied within the DS GeneAtlas pipeline, has been used to critically evaluate the severe acute respiratory syndrome (SARS) genome with the goal of identifying new potential targets for viral therapeutic intervention. This paper discusses several new functional hypotheses on the roles played by the constituent gene products of SARS, and will serve as an example of how such assignments can be developed or extended on other systems of interest.

Sex hormone-binding globulin in the human prostate is locally synthesized and may act as an autocrine/paracrine effector.

Sex hormone-binding globulin (SHBG) is a plasma protein synthesized and secreted by the liver. Its initial description stemmed from its ability to bind estrogens and androgens and its capacity to regulate the free concentration of the steroids that bind to it. Additionally, it participates in signal transduction for certain steroid hormones at the cell membrane. It binds with high affinity to a specific membrane receptor (R(SHBG)) in prostate stromal and epithelial cells, wherein the SHBG.R(SHBG) complex forms. An appropriate steroid binds to this complex and results in increases of intracellular cAMP. These two disparate functions of SHBG, regulation of the concentration of free steroids in plasma and signal transduction in selected tissues, raise the question of how its synthesis and secretion might be regulated so as to best perform these two disparate functions. In this paper we demonstrate that SHBG is produced in human prostate cancer cell lines (LNCaP, DU 145, and PC 3) as well as in cultured human prostate epithelial and stromal cells. In addition, in tissue sections of human prostate, we demonstrate the presence of SHBG (immunocytochemistry) and SHBG mRNA (in situ hybridization). These observations are consistent with the hypothesis that SHBG, destined to participate in signaling at the cell membrane, is locally regulated and produced.