Deborah R. Gordon

Bio: Deborah R. Gordon is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: Nursing care & Ideology. The author has an hindex of 13, co-authored 20 publications receiving 3849 citations.

Integrating common and rare genetic variation in diverse human populations

Abstract: Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of

The Phenomenology of Knowing the Patient

Abstract: Nurses' discourse about knowing the patient emerged as a recurring theme in an interpretive phenomenological study of the development of expertise in critical care nursing. The purpose of this article is to present analyses related to the meaning of knowing the patient, and its role in everyday nursing practice. Informants in the study were 130 nurses who practiced in adult, pediatric and newborn intensive care units of eight hospitals in three metropolitan areas. The data were group interviews in which nurses gave narrative accounts of exemplars from their practice; in addition, a sub-sample of 48 nurses were observed in their practice and participated in intensive personal history interviews. Knowing the patient means both knowing the patient's typical pattern of responses and knowing the patient as a person. Knowing the patient is central to skilled clinical judgment, requires involvement, and sets up the possibility for patient advocacy and for learning about patient populations.

Tenacious Assumptions in Western Medicine

Abstract: While biomedicine has successfully created and hoarded a body of technical knowledge to call its own, its knowledge and practices draw upon a background of tacit understandings that extend far beyond medical boundaries The biological reductionism by which modern medicine is frequently characterized is more theoretical than actual; in its effects, biomedicine speaks beyond its explicit reductionist reference through the implicit ways it teaches us to interpret ourselves, our world, and the rela-tionships between humans, nature, self, and society It draws upon and projects cosmology (ways of ordering the world), ontology (assumptions about reality and being), epistemology (assumptions about knowledge and truth), understandings of personhood, society, morality, and religion (what is sacred and profane) Although biomedicine both constitutes and is constituted by society, this interdependency is nevertheless denied by biomedical theory and ideology which claim neutrality and universality

Embodying illness, embodying cancer.

Abstract: Individuals and societies embody illnesses in different ways, in part determined by the way a person knows and lives his or her diagnosis and prognosis. Based on research in Northern Italy, on the experiences and meanings of cancer and on the practice of nondisclosure of the diagnosis, we find nondisclosure reflects a world divided--life/death, good/bad, mind/body--with the unwanted converted to "other." The strong association of cancer with death, suffering, and hopelessness in much of Italy, coupled with the tremendous power attributed to naming and "sentencing" makes nondisclosure a major mechanism for keeping the "condemned" in this social world, and keeping death, decay, and suffering in the "other." It is the social reality that is dominant here, such that informing a patient of cancer can be tantamount to social death.

A Map of Human Genome Variation From Population-Scale Sequencing

Abstract: The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

Abstract: This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK.

Qualitative methods for health research

Abstract: Qualitative methods for health research , Qualitative methods for health research , کتابخانه مرکزی دانشگاه علوم پزشکی تهران

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

Abstract: Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysi...

LD score regression distinguishes confounding from polygenicity in genome-wide association studies :

Abstract: Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from a true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size.