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1.
Am J Hum Genet ; 111(3): 412-423, 2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38458162

ABSTRACT

This article is based on the address given by the author at the 2023 meeting of The American Society of Human Genetics (ASHG). A video of the original address can be found at the ASHG website.


Subject(s)
Awards and Prizes , Humans , United States , Achievement
2.
Nature ; 577(7789): 179-189, 2020 01.
Article in English | MEDLINE | ID: mdl-31915397

ABSTRACT

A primary goal of human genetics is to identify DNA sequence variants that influence biomedical traits, particularly those related to the onset and progression of human disease. Over the past 25 years, progress in realizing this objective has been transformed by advances in technology, foundational genomic resources and analytical tools, and by access to vast amounts of genotype and phenotype data. Genetic discoveries have substantially improved our understanding of the mechanisms responsible for many rare and common diseases and driven development of novel preventative and therapeutic strategies. Medical innovation will increasingly focus on delivering care tailored to individual patterns of genetic predisposition.


Subject(s)
Genetic Variation , Animals , Genetic Testing , Genomics , Genotype , Humans , Phenotype , Rare Diseases/genetics
3.
Hum Mol Genet ; 29(11): 1922-1932, 2020 07 21.
Article in English | MEDLINE | ID: mdl-32436959

ABSTRACT

Hundreds of loci have been associated with blood pressure (BP) traits from many genome-wide association studies. We identified an enrichment of these loci in aorta and tibial artery expression quantitative trait loci in our previous work in ~100 000 Genetic Epidemiology Research on Aging study participants. In the present study, we sought to fine-map known loci and identify novel genes by determining putative regulatory regions for these and other tissues relevant to BP. We constructed maps of putative cis-regulatory elements (CREs) using publicly available open chromatin data for the heart, aorta and tibial arteries, and multiple kidney cell types. Variants within these regions may be evaluated quantitatively for their tissue- or cell-type-specific regulatory impact using deltaSVM functional scores, as described in our previous work. We aggregate variants within these putative CREs within 50 Kb of the start or end of 'expressed' genes in these tissues or cell types using public expression data and use deltaSVM scores as weights in the group-wise sequence kernel association test to identify candidates. We test for association with both BP traits and expression within these tissues or cell types of interest and identify the candidates MTHFR, C10orf32, CSK, NOV, ULK4, SDCCAG8, SCAMP5, RPP25, HDGFRP3, VPS37B and PPCDC. Additionally, we examined two known QT interval genes, SCN5A and NOS1AP, in the Atherosclerosis Risk in Communities Study, as a positive control, and observed the expected heart-specific effect. Thus, our method identifies variants and genes for further functional testing using tissue- or cell-type-specific putative regulatory information.


Subject(s)
Atherosclerosis/genetics , Blood Pressure/genetics , Quantitative Trait Loci/genetics , Regulatory Sequences, Nucleic Acid/genetics , Aorta/physiopathology , Atherosclerosis/physiopathology , Blood Pressure/physiology , Chromatin , Gene Expression Regulation/genetics , Genome-Wide Association Study , Heart/physiopathology , Humans , Intracellular Signaling Peptides and Proteins/genetics , Kidney/physiopathology , Membrane Proteins/genetics , Tibial Arteries/physiopathology
4.
Genet Med ; 24(2): 410-418, 2022 02.
Article in English | MEDLINE | ID: mdl-34906477

ABSTRACT

PURPOSE: This study aimed to understand broad data sharing decisions among predominantly underserved families participating in genomic research. METHODS: Drawing on clinic observations, semistructured interviews, and survey data from prenatal and pediatric families enrolled in a genomic medicine study focused on historically underserved and underrepresented populations, this paper expands empirical evidence regarding genomic data sharing communication and decision-making. RESULTS: One-third of parents declined to share family data, and pediatric participants were significantly more likely to decline than prenatal participants. The pediatric population was significantly more socioeconomically disadvantaged and more likely to require interpreters. Opt-in was tied to altruism and participants' perception that data sharing was inherent to research participation. Opt-out was associated with privacy concerns and influenced by clinical staff's presentation of data handling procedures. The ability of participants to make informed choices during enrollment about data sharing was weakened by suboptimal circumstances, which was revealed by poor understanding of data sharing in follow-up interviews as well as discrepancies between expressed participant desires and official recorded choices. CONCLUSION: These empirical data suggest that the context within which informed consent process is conducted in clinical genomics may be inadequate for respecting participants' values and preferences and does not support informed decision-making processes.


Subject(s)
Genomic Medicine , Informed Consent , Child , Genomics , Humans , Information Dissemination , Privacy
5.
Cardiovasc Diabetol ; 21(1): 132, 2022 07 14.
Article in English | MEDLINE | ID: mdl-35836181

ABSTRACT

BACKGROUND: Prior studies of the glycemic effect of statins have been inconsistent. Also, most studies have only considered a short duration of statin use; the effect of long-term statin use on fasting glucose (FG) has not been well examined. The aim of this work is to investigate the effect of long-term statin exposure on FG levels. METHODS: Using electronic health record (EHR) data from a large and diverse longitudinal cohort, we defined long-term statin exposure in two ways: the cumulative years of statin use (cumulative supply) and the years' supply-weighted sum of doses (cumulative dose). Simvastatin, lovastatin, atorvastatin and pravastatin were included in the analysis. The relationship between statin exposure and FG was examined using linear regression with mixed effects modeling, comparing statin users before and after initiating statins and statin never-users. RESULTS: We examined 593,130 FG measurements from 87,151 individuals over a median follow up of 20 years. Of these, 42,678 were never-users and 44,473 were statin users with a total of 730,031 statin prescriptions. FG was positively associated with cumulative supply of statin but not comulative dose when both measures were in the same model. While statistically significant, the annual increase in FG attributable to statin exposure was modest at only 0.14 mg/dl, with only slight and non-significant differences among statin types. CONCLUSIONS: Elevation in FG level is associated with statin exposure, but the effect is modest. The results suggest that the risk of a clinically significant increase in FG attributable to long-term statin use is small for most individuals.


Subject(s)
Hydroxymethylglutaryl-CoA Reductase Inhibitors , Atorvastatin/adverse effects , Electronic Health Records , Fasting , Glucose , Humans , Hydroxymethylglutaryl-CoA Reductase Inhibitors/adverse effects
6.
Ann Noninvasive Electrocardiol ; 27(1): e12888, 2022 01.
Article in English | MEDLINE | ID: mdl-34547155

ABSTRACT

BACKGROUND: TdP is a form of polymorphic ventricular tachycardia which develops in the setting of a prolonged QT interval. There are limited data describing risk factors, treatment, and outcomes of this potentially fatal arrhythmia. OBJECTIVE: Our goals were as follows: (1) to validate cases presenting with Torsade de Pointes (TdP), (2) to identify modifiable risk factors, and (3) to describe the management strategies used for TdP and its prognosis in a real-world healthcare setting. METHODS: Case-control study (with 2:1 matching on age, sex, and race/ethnicity) nested within the Genetic Epidemiology Research on Aging (GERA) cohort. Follow-up of the cohort for case ascertainment was between January 01, 2005 and December 31, 2018. RESULTS: A total of 56 cases of TdP were confirmed (incidence rate = 3.6 per 100,000 persons/years). The average (SD) age of the TdP cases was 74 (13) years, 55 percent were female, and 16 percent were non-white. The independent predictors of TdP were potassium concentration <3.6 mEq/L (OR = 10.6), prior history of atrial fibrillation/flutter (OR = 6.2), QTc >480 ms (OR = 4.4) and prior history of coronary artery disease (OR = 2.6). Exposure to furosemide and amiodarone was significantly greater in cases than in controls. The most common treatment for TdP was IV magnesium (78.6%) and IV potassium repletion (73.2%). The in-hospital and 1-year mortality rates for TdP cases were 10.7% and 25.0% percent, respectively. CONCLUSIONS: These findings may inform quantitative multivariate risk indices for the prediction of TdP and could guide practitioners on which patients may qualify for continuous ECG monitoring and/or electrolyte replacement therapy.


Subject(s)
Delivery of Health Care, Integrated , Long QT Syndrome , Torsades de Pointes , Aged , Case-Control Studies , Electrocardiography , Female , Humans , Torsades de Pointes/diagnosis , Torsades de Pointes/epidemiology
7.
Am J Hum Genet ; 103(3): 319-327, 2018 09 06.
Article in English | MEDLINE | ID: mdl-30193136

ABSTRACT

The Clinical Sequencing Evidence-Generating Research (CSER) consortium, now in its second funding cycle, is investigating the effectiveness of integrating genomic (exome or genome) sequencing into the clinical care of diverse and medically underserved individuals in a variety of healthcare settings and disease states. The consortium comprises a coordinating center, six funded extramural clinical projects, and an ongoing National Human Genome Research Institute (NHGRI) intramural project. Collectively, these projects aim to enroll and sequence over 6,100 participants in four years. At least 60% of participants will be of non-European ancestry or from underserved settings, with the goal of diversifying the populations that are providing an evidence base for genomic medicine. Five of the six clinical projects are enrolling pediatric patients with various phenotypes. One of these five projects is also enrolling couples whose fetus has a structural anomaly, and the sixth project is enrolling adults at risk for hereditary cancer. The ongoing NHGRI intramural project has enrolled primarily healthy adults. Goals of the consortium include assessing the clinical utility of genomic sequencing, exploring medical follow up and cascade testing of relatives, and evaluating patient-provider-laboratory level interactions that influence the use of this technology. The findings from the CSER consortium will offer patients, healthcare systems, and policymakers a clearer understanding of the opportunities and challenges of providing genomic medicine in diverse populations and settings, and contribute evidence toward developing best practices for the delivery of clinically useful and cost-effective genomic sequencing in diverse healthcare settings.


Subject(s)
Genome, Human/genetics , Adult , Cost-Benefit Analysis/methods , Delivery of Health Care/methods , Europe , Exome/genetics , Genomics/methods , Humans , National Human Genome Research Institute (U.S.) , Phenotype , United States , Whole Genome Sequencing/methods
8.
Prenat Diagn ; 41(9): 1049-1056, 2021 Aug.
Article in English | MEDLINE | ID: mdl-34057205

ABSTRACT

The probability an individual is a carrier for a recessive disorder despite a negative carrier test, referred to as residual risk, has been part of carrier screening for over 2 decades. Residual risks are calculated by subtracting the frequency of carriers of pathogenic variants detected by the test from the carrier frequency in a population, estimated from the incidence of the disease. Estimates of the incidence (and therefore carrier frequency) of many recessive disorders differ among different population groups and are inaccurate or unavailable for many genes on large carrier screening panels for most of the world's populations. The pathogenic variants detected by the test and their frequencies also vary across groups and over time as variants are newly discovered or reclassified, which requires today's residual carrier risks to be continually updated. Even when a residual carrier risk is derived using accurate data obtained in a particular group, it may not apply to many individuals in that group because of misattributed ancestry or unsuspected admixture. Missing or inaccurate data, the challenge of determining meaningful ancestry-specific risks and applying them appropriately, and a lack of evidence they impact management, suggest that patients be counseled that although carrier screening may miss a small fraction of carriers, residual risks with contemporary carrier screening are well below the risk posed by invasive prenatal diagnosis, even if one member of the couple is a carrier, and that efforts to provide precise residual carrier risks are unnecessary.


Subject(s)
Cystic Fibrosis/genetics , Genetic Carrier Screening/methods , Cystic Fibrosis/diagnosis , Genetic Carrier Screening/trends , Humans , Risk Assessment/methods , Risk Assessment/standards
9.
J Allergy Clin Immunol ; 145(1): 192-198.e11, 2020 01.
Article in English | MEDLINE | ID: mdl-31369801

ABSTRACT

BACKGROUND: Atopic dermatitis (AD) is more common among African American children. Whether there are racial/ethnic difference among adults with AD and the causes for those disparities are unclear. OBJECTIVE: We sought to examine the relationship between self-reported race/ethnicity and AD and determine whether African genetic ancestry is predictive of these outcomes among African American subjects. METHODS: We analyzed data from 2 independent multiethnic longitudinal studies: 86,893 subjects aged 18 to 100 years from the Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort and 5467 subjects aged 2 to 26 years from the national Pediatric Eczema Elective Registry (PEER) cohort. The primary outcomes were physician-diagnosed AD in GERA and repeated measures of self-reported disease control among patients with physician-diagnosed AD at 6-month intervals in PEER. We examined whether self-identified African American race/ethnicity was predictive of these outcomes and then tested whether a continuous measure of African genetic ancestry was associated with outcomes within the African American group. RESULTS: AD was more common among self-identified African American subjects than non-Hispanic white subjects in GERA (4.4% vs 2.1%; odds ratio, 2.06; 95% CI, 1.70-2.48) and less well-controlled in PEER subjects (odds of 1-level worse control, 1.91; 95% CI, 1.64-2.22). However, African genetic ancestry was not associated with AD risk or control among self-identified African American subjects in either cohort, nor did an AD polygenic risk score or genetic skin pigment score explain the AD disparities in patients with AD. CONCLUSION: Ancestry-related genetic effects do not explain increased AD prevalence or poorer disease control among African American subjects.


Subject(s)
Black or African American/genetics , Dermatitis, Atopic/epidemiology , Dermatitis, Atopic/genetics , Aged , Cohort Studies , Dermatitis, Atopic/pathology , Disease Susceptibility , Female , Humans , Male , Middle Aged , Prevalence , United States
10.
Am J Med Genet A ; 182(3): 513-520, 2020 03.
Article in English | MEDLINE | ID: mdl-31880405

ABSTRACT

We describe an 11-year old boy with severe global developmental delays, failure to thrive and growth retardation, refractory seizures with recurrent status epilepticus, hypogammaglobulinemia, hypergonadotropic hypogonadism, and duodenal strictures. He had facial and skin findings compatible with trichothiodystrophy, including sparse and brittle hair, thin eyebrows, and dry skin. Exome sequencing showed a hemizygous, truncating variant in RNF113A, c.903_910delGCAGACCA, predicting p.(Gln302fs*12), that was inherited from his mother. Although his clinical features overlap closely with features described in the two previously reported male first cousins with RNF113A loss of function mutations, the duodenal strictures seen in this patient have not been reported. Interestingly, the patient's mother had short stature and 100% skewed X-inactivation as seen in other obligate female carriers. A second male with developmental delays, microcephaly, seizures, ambiguous genitalia, and facial anomalies that included sparse and brittle hair, thin eyebrows and dry skin was recently reported to have c.897_898delTG, predicting p.(Cys299*) in RNF113A and we provide additional clinical details for this patient. This report further supports deleterious variants in RNF113A as a cause of a novel trichothiodystrophy syndrome.


Subject(s)
DNA-Binding Proteins/genetics , Genetic Diseases, X-Linked/genetics , Genetic Predisposition to Disease , Trichothiodystrophy Syndromes/genetics , Child , Child, Preschool , Female , Genetic Association Studies , Genetic Diseases, X-Linked/diagnosis , Genetic Diseases, X-Linked/pathology , Humans , Male , Mutation/genetics , Trichothiodystrophy Syndromes/diagnosis , Trichothiodystrophy Syndromes/pathology , X Chromosome Inactivation/genetics
11.
PLoS Genet ; 13(4): e1006655, 2017 04.
Article in English | MEDLINE | ID: mdl-28384154

ABSTRACT

Genetic similarity of spouses can reflect factors influencing mate choice, such as physical/behavioral characteristics, and patterns of social endogamy. Spouse correlations for both genetic ancestry and measured traits may impact genotype distributions (Hardy Weinberg and linkage equilibrium), and therefore genetic association studies. Here we evaluate white spouse-pairs from the Framingham Heart Study (FHS) original and offspring cohorts (N = 124 and 755, respectively) to explore spousal genetic similarity and its consequences. Two principal components (PCs) of the genome-wide association (GWA) data were identified, with the first (PC1) delineating clines of Northern/Western to Southern European ancestry and the second (PC2) delineating clines of Ashkenazi Jewish ancestry. In the original (older) cohort, there was a striking positive correlation between the spouses in PC1 (r = 0.73, P = 3x10(-22)) and also for PC2 (r = 0.80, P = 7x10(-29)). In the offspring cohort, the spouse correlations were lower but still highly significant for PC1 (r = 0.38, P = 7x10(-28)) and for PC2 (r = 0.45, P = 2x10(-39)). We observed significant Hardy-Weinberg disequilibrium for single nucleotide polymorphisms (SNPs) loading heavily on PC1 and PC2 across 3 generations, and also significant linkage disequilibrium between unlinked SNPs; both decreased with time, consistent with reduced ancestral endogamy over generations and congruent with theoretical calculations. Ignoring ancestry, estimates of spouse kinship have a mean significantly greater than 0, and more so in the earlier generations. Adjusting kinship estimates for genetic ancestry through the use of PCs led to a mean spouse kinship not different from 0, demonstrating that spouse genetic similarity could be fully attributed to ancestral assortative mating. These findings also have significance for studies of heritability that are based on distantly related individuals (kinship less than 0.05), as we also demonstrate the poor correlation of kinship estimates in that range when ancestry is or is not taken into account.


Subject(s)
Genome-Wide Association Study , Spouses , White People/genetics , Female , Genome, Human , Genotype , Humans , Jews/genetics , Linkage Disequilibrium , Male , Phenotype , Polymorphism, Single Nucleotide
12.
Pharmacogenet Genomics ; 29(8): 192-199, 2019 10.
Article in English | MEDLINE | ID: mdl-31461080

ABSTRACT

OBJECTIVE: To assess the impact of CYP2C9 variation on phenytoin patient response and clinician prescribing practice where genotype was unknown during treatment. METHODS: A retrospective analysis of Resource on Genetic Epidemiology Research on Adult Health and Aging cohort participants who filled a phenytoin prescription between 1996 and 2017. We used laboratory test results, medication dispensing records, and medical notes to identify associations of CYP2C9 genotype with phenytoin blood concentration, neurologic side effects, and medication dispensing patterns reflecting clinician prescribing practice and patient response. RESULTS: Among 993 participants, we identified 69% extensive, 20% high-intermediate, 10% low-intermediate, and 2% poor metabolizers based on CYP2C9 genotypes. Compared with extensive metabolizer genotype, low-intermediate/poor metabolizer genotype was associated with increased dose-adjusted phenytoin blood concentration [21.3 pg/mL, 95% confidence interval (CI): 13.6-29.0 pg/mL; P < 0.01] and increased risk of neurologic side effects (hazard ratio: 2.40, 95% CI: 1.24-4.64; P < 0.01). Decreased function CYP2C9 genotypes were associated with medication dispensing patterns indicating dose decrease, use of alternative anticonvulsants, and worse adherence, although these associations varied by treatment indication for phenytoin. CONCLUSION: CYP2C9 variation was associated with clinically meaningful differences in clinician prescribing practice and patient response, with potential implications for healthcare utilization and treatment efficacy.


Subject(s)
Cytochrome P-450 CYP2C9/genetics , Pharmacogenomic Variants , Phenytoin/administration & dosage , Adult , Aged , Aged, 80 and over , Delivery of Health Care, Integrated , Dose-Response Relationship, Drug , Electronic Health Records , Female , Humans , Male , Medication Adherence , Middle Aged , Pharmacogenomic Testing , Phenytoin/pharmacokinetics , Practice Patterns, Physicians' , Retrospective Studies , Treatment Outcome
14.
PLoS Genet ; 12(10): e1006371, 2016 Oct.
Article in English | MEDLINE | ID: mdl-27764096

ABSTRACT

Age-related hearing impairment (ARHI), one of the most common sensory disorders, can be mitigated, but not cured or eliminated. To identify genetic influences underlying ARHI, we conducted a genome-wide association study of ARHI in 6,527 cases and 45,882 controls among the non-Hispanic whites from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We identified two novel genome-wide significant SNPs: rs4932196 (odds ratio = 1.185, p = 4.0x10-11), 52Kb 3' of ISG20, which replicated in a meta-analysis of the other GERA race/ethnicity groups (1,025 cases, 12,388 controls, p = 0.00094) and in a UK Biobank case-control analysis (30,802 self-reported cases, 78,586 controls, p = 0.015); and rs58389158 (odds ratio = 1.132, p = 1.8x10-9), which replicated in the UK Biobank (p = 0.00021). The latter SNP lies just outside exon 8 and is highly correlated (r2 = 0.96) with the missense SNP rs5756795 in exon 7 of TRIOBP, a gene previously associated with prelingual nonsyndromic hearing loss. We further tested these SNPs in phenotypes from audiologist notes available on a subset of GERA (4,903 individuals), stratified by case/control status, to construct an independent replication test, and found a significant effect of rs58389158 on speech reception threshold (SRT; overall GERA meta-analysis p = 1.9x10-6). We also tested variants within exons of 132 other previously-identified hearing loss genes, and identified two common additional significant SNPs: rs2877561 (synonymous change in ILDR1, p = 6.2x10-5), which replicated in the UK Biobank (p = 0.00057), and had a significant GERA SRT (p = 0.00019) and speech discrimination score (SDS; p = 0.0019); and rs9493627 (missense change in EYA4, p = 0.00011) which replicated in the UK Biobank (p = 0.0095), other GERA groups (p = 0.0080), and had a consistent significant result for SRT (p = 0.041) and suggestive result for SDS (p = 0.081). Large cohorts with GWAS data and electronic health records may be a useful method to characterize the genetic architecture of ARHI.


Subject(s)
Exonucleases/genetics , Hearing Loss/genetics , Microfilament Proteins/genetics , Presbycusis/genetics , Receptors, Cell Surface/genetics , Trans-Activators/genetics , Adult , Aging/genetics , Aging/pathology , Electronic Health Records , Ethnicity , Exoribonucleases , Female , Genetic Predisposition to Disease , Genome-Wide Association Study , Genotype , Hearing Loss/epidemiology , Hearing Loss/pathology , Humans , Male , Phenotype , Polymorphism, Single Nucleotide , Presbycusis/epidemiology , Presbycusis/pathology
15.
PLoS Genet ; 11(1): e1004930, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25629170

ABSTRACT

An efficient approach to characterizing the disease burden of rare genetic variants is to impute them into large well-phenotyped cohorts with existing genome-wide genotype data using large sequenced referenced panels. The success of this approach hinges on the accuracy of rare variant imputation, which remains controversial. For example, a recent study suggested that one cannot adequately impute the HOXB13 G84E mutation associated with prostate cancer risk (carrier frequency of 0.0034 in European ancestry participants in the 1000 Genomes Project). We show that by utilizing the 1000 Genomes Project data plus an enriched reference panel of mutation carriers we were able to accurately impute the G84E mutation into a large cohort of 83,285 non-Hispanic White participants from the Kaiser Permanente Research Program on Genes, Environment and Health Genetic Epidemiology Research on Adult Health and Aging cohort. Imputation authenticity was confirmed via a novel classification and regression tree method, and then empirically validated analyzing a subset of these subjects plus an additional 1,789 men from Kaiser specifically genotyped for the G84E mutation (r2 = 0.57, 95% CI = 0.37­0.77). We then show the value of this approach by using the imputed data to investigate the impact of the G84E mutation on age-specific prostate cancer risk and on risk of fourteen other cancers in the cohort. The age-specific risk of prostate cancer among G84E mutation carriers was higher than among non-carriers. Risk estimates from Kaplan-Meier curves were 36.7% versus 13.6% by age 72, and 64.2% versus 24.2% by age 80, for G84E mutation carriers and non-carriers, respectively (p = 3.4x10-12). The G84E mutation was also associated with an increase in risk for the fourteen other most common cancers considered collectively (p = 5.8x10-4) and more so in cases diagnosed with multiple cancer types, both those including and not including prostate cancer, strongly suggesting pleiotropic effects. [corrected].


Subject(s)
Homeodomain Proteins/genetics , Prostatic Neoplasms/epidemiology , Prostatic Neoplasms/genetics , Adult , Aged , Aged, 80 and over , California , Genetic Predisposition to Disease , Genome-Wide Association Study , Germ-Line Mutation , Haplotypes , Humans , Male , Middle Aged , Phylogeny , Polymorphism, Single Nucleotide , Prostatic Neoplasms/pathology , Risk Factors
16.
Genome Res ; 24(11): 1734-9, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25304867

ABSTRACT

Exome and whole-genome sequencing studies are becoming increasingly common, but little is known about the accuracy of the genotype calls made by the commonly used platforms. Here we use replicate high-coverage sequencing of blood and saliva DNA samples from four European-American individuals to estimate lower bounds on the error rates of Complete Genomics and Illumina HiSeq whole-genome and whole-exome sequencing. Error rates for nonreference genotype calls range from 0.1% to 0.6%, depending on the platform and the depth of coverage. Additionally, we found (1) no difference in the error profiles or rates between blood and saliva samples; (2) Complete Genomics sequences had substantially higher error rates than Illumina sequences had; (3) error rates were higher (up to 6%) for rare or unique variants; (4) error rates generally declined with genotype quality (GQ) score, but in a nonlinear fashion for the Illumina data, likely due to loss of specificity of GQ scores greater than 60; and (5) error rates increased with increasing depth of coverage for the Illumina data. These findings, especially (3)-(5), suggest that caution should be taken in interpreting the results of next-generation sequencing-based association studies, and even more so in clinical application of this technology in the absence of validation by other more robust sequencing or genotyping methods.


Subject(s)
Exome/genetics , Genomics/methods , Genotyping Techniques/methods , High-Throughput Nucleotide Sequencing/methods , Gene Frequency , Genome, Human/genetics , Genotype , Humans , Polymorphism, Single Nucleotide , Reproducibility of Results , White People/genetics
17.
Hum Mol Genet ; 23(24): 6634-43, 2014 Dec 15.
Article in English | MEDLINE | ID: mdl-25027321

ABSTRACT

We report a genome-wide association study (GWAS) and admixture analysis of glaucoma in 12 008 African-American and Hispanic women (age 50-79 years) from the Women's Health Initiative (WHI). Although GWAS of glaucoma have been conducted on several populations, this is the first to look at glaucoma in individuals of African-American and Hispanic race/ethnicity. Prevalent and incident glaucoma was determined by self-report from study questionnaires administered at baseline (1993-1998) and annually through 2005. For African Americans, there was a total of 658 prevalent cases, 1062 incident cases and 6067 individuals who never progressed to glaucoma. For our replication cohort, we used the WHI Hispanics, including 153 prevalent cases, 336 incident cases and 2685 non-cases. We found an association of African ancestry with glaucoma incidence in African Americans (hazards ratio 1.62, 95% CI 1.023-2.56, P = 0.038) and in Hispanics (hazards ratio 3.21, 95% CI 1.32-7.80, P = 0.011). Although we found that no previously identified glaucoma SNPs replicated in either the WHI African Americans or Hispanics, a risk score combining all previously reported hits was significant in African-American prevalent cases (P = 0.0046), and was in the expected direction in the incident cases, as well as in the Hispanic incident cases. Additionally, after imputing to 1000 Genomes, two less common independent SNPs were suggestive in African Americans, but had too low of an allele frequency in Hispanics to test for replication. These results suggest the possibility of a distinct genetic architecture underlying glaucoma in individuals of African ancestry.


Subject(s)
Alleles , Genetic Loci , Glaucoma/ethnology , Glaucoma/genetics , Polymorphism, Single Nucleotide , Black or African American , Aged , Female , Gene Frequency , Genome-Wide Association Study , Glaucoma/epidemiology , Glaucoma/pathology , Hispanic or Latino , Humans , Incidence , Middle Aged , Odds Ratio , Prevalence , Risk , Self Report , Surveys and Questionnaires , United States/epidemiology , Women's Health
19.
Am J Hum Genet ; 92(6): 904-16, 2013 Jun 06.
Article in English | MEDLINE | ID: mdl-23726366

ABSTRACT

Blood lipid concentrations are heritable risk factors associated with atherosclerosis and cardiovascular diseases. Lipid traits exhibit considerable variation among populations of distinct ancestral origin as well as between individuals within a population. We performed association analyses to identify genetic loci influencing lipid concentrations in African American and Hispanic American women in the Women's Health Initiative SNP Health Association Resource. We validated one African-specific high-density lipoprotein cholesterol locus at CD36 as well as 14 known lipid loci that have been previously implicated in studies of European populations. Moreover, we demonstrate striking similarities in genetic architecture (loci influencing the trait, direction and magnitude of genetic effects, and proportions of phenotypic variation explained) of lipid traits across populations. In particular, we found that a disproportionate fraction of lipid variation in African Americans and Hispanic Americans can be attributed to genomic loci exhibiting statistical evidence of association in Europeans, even though the precise genes and variants remain unknown. At the same time, we found substantial allelic heterogeneity within shared loci, characterized both by population-specific rare variants and variants shared among multiple populations that occur at disparate frequencies. The allelic heterogeneity emphasizes the importance of including diverse populations in future genetic association studies of complex traits such as lipids; furthermore, the overlap in lipid loci across populations of diverse ancestral origin argues that additional knowledge can be gleaned from multiple populations.


Subject(s)
Lipids/blood , Black or African American/genetics , Aged , Chromosomes, Human , Female , Genetic Loci , Genome-Wide Association Study , Hispanic or Latino/genetics , Humans , Middle Aged , Models, Genetic , Polymorphism, Single Nucleotide
20.
Ophthalmology ; 123(1): 92-101, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26260281

ABSTRACT

PURPOSE: To evaluate the association between refractive error and the prevalence of glaucoma by race or ethnicity. DESIGN: Cross-sectional study. PARTICIPANTS: Kaiser Permanente Northern California Health Plan members with refractive error measured at 35 years of age or older between 2008 and 2014 and with no history of cataract surgery, refractive surgery, or a corneal disorder. METHODS: We identified 34 040 members with glaucoma or ocular hypertension (OHTN; cases) and 403 398 members without glaucoma (controls). Glaucoma cases were classified as primary angle-closure glaucoma (PACG); 1 of the 4 forms of open-angle glaucoma: primary open-angle glaucoma (POAG), normal-tension glaucoma (NTG), pigmentary glaucoma (PIGM), and pseudoexfoliation glaucoma (PEX); or OHTN. Refractive error, expressed as spherical equivalent (SE), was coded as a continuous trait and also as categories. Logistic regression analyses were used to estimate the association between refractive error and the prevalence of glaucoma overall and in specific racial or ethnic groups. MAIN OUTCOME MEASURES: The association between refractive error and glaucoma subtypes evaluated as odds ratios (ORs) with 95% confidence intervals (CIs). RESULTS: In controls, the mean SE was -0.59 diopters (D) (standard deviation, 2.62 D). Each 1-D reduction in SE was associated with a 22% decrease in the odds of PACG (OR, 0.78; 95% CI, 0.77-0.80) and with increases in the odds of open-angle glaucoma ranging from 1.23 (95% CI, 1.20-1.26) for PIGM, to 1.07 (95% CI, 1.03-1.11) for PEX, and to 1.05 (95% CI, 1.04-1.06) for OHTN. In addition, we observed a stronger association between myopia and POAG among non-Hispanic whites (OR, 1.12; 95% CI, 1.11-1.13) and NTG among Asians (OR, 1.17; 95% CI, 1.15-1.20) and non-Hispanic whites (OR, 1.19; 95% CI, 1.15-1.22). CONCLUSIONS: Myopia was associated with an increased prevalence of all forms of open-angle glaucoma and OHTN, whereas hyperopia was associated with a substantially increased prevalence of PACG. Although high myopia is a strong risk factor for glaucoma subtypes, low and moderate myopia also have a significant effect on glaucoma risk. Additionally, there were moderate racial differences in the association of myopia with the risk of POAG and NTG.


Subject(s)
Ethnicity , Glaucoma/ethnology , Refraction, Ocular/physiology , Refractive Errors/ethnology , Adult , Aged , California/epidemiology , Cross-Sectional Studies , Female , Glaucoma/complications , Glaucoma/physiopathology , Humans , Incidence , Intraocular Pressure/physiology , Male , Middle Aged , Prevalence , Refractive Errors/etiology , Refractive Errors/physiopathology , Retrospective Studies
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