Dataset Information

Platinum-Quality Mitogenome Haplotypes from United States Populations.

ABSTRACT: A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95% of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories.

SUBMITTER: Taylor CR

PROVIDER: S-EPMC7716222 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Platinum-Quality Mitogenome Haplotypes from United States Populations.

Taylor Cassandra R CR Kiesler Kevin M KM Sturk-Andreaggi Kimberly K Ring Joseph D JD Parson Walther W Schanfield Moses M Vallone Peter M PM Marshall Charla C

Genes 20201029 11

A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth o ...[more]

PMID: 33138247

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Project description:ObjectivesThis article aims to examine the disparities in dental service utilization among 3 age groups: younger adults (20-49 y), middle-aged adults (50-64 y), and older adults (65+ y), among Whites, Hispanics, Blacks, Asians, American Indians or Alaska Natives (AIAN), and Native Hawaiian or other Pacific Islanders (NHOPI).MethodsWeighted logistic regression models were conducted to analyze 9 waves of cross-sectional survey data (2002-2018) from the Behavioral Risk Factor Surveillance System. We estimated age group- and race/ethnic-specific prevalences of dental service utilization adjusting sociodemographics and self-rated health for each wave and compared with crude analysis. Next, we performed linear regression analysis of the trend of adjusted prevalences over time and the average level by race/ethnicity and age groups.ResultsRacial/ethnic disparities increased with age, even though the adjusted prevalences of dental service utilization were less apparent than the crude analysis. The all-wave average prevalence was 71%. Black older adults had the lowest level of dental service utilization (65%) as compared with the 2 highest groups: White older adults (79%) and Asian older adults (76%). The general younger adult populations had low prevalences, with the lowest among Asian younger adults (65%). AIAN and NHOPI individuals from all age groups tended to have average or below average prevalences. In addition, a decreasing trend of dental service utilization was observed among White individuals of all age groups (0.2%-0.3% lower per year, P < 0.01) and AIAN younger adults (0.5% lower per year, P < 0.01).ConclusionHealth policy, federal funding, and community-based programs should address the needs of dental service utilization for racial/ethnic minorities including Blacks, AIANs, and NHOPIs.Knowledge transfer statementOur study offers insights into our understanding of disparities in dental service utilization among minority racial/ethnic groups. As health policy, federal funding, and community-based programs seek to improve oral health, there is a need to address access to and utilization of dental service for Blacks, American Indians or Alaska Natives, and Native Hawaiian or other Pacific Islanders.

Project description:Introduction: Fine wool production is an important source of revenue, accounting for up to 13% of total revenue in extensively managed wool sheep production systems of the United States. The Rambouillet are a predominant breed that excels in wool quality characteristics. Understanding the genetic basis of wool quality characteristics would aid in the development of genomic breeding strategies to facilitate genetic improvement. Methods: Wool characteristics and DNA were collected for rams enrolled in the North Dakota State University and University of Wyoming annual central performance ram tests over a three-year period (2019–2021, N = 313). The relationships of wool quality characteristics including grease fleece weight adjusted 365 days (wt. 365 adj.), clean fleece wt. 365 adj., staple length 365 adj., average fiber diameter, face wool cover, amount of skin wrinkles and belly wool were evaluated through genome-wide association studies (GWAS), Pearson correlation and ANOVA. Results: The GWAS identified four genome-wide significant genetic markers (p-value <1.19e-06) and five chromosome-wide significant markers (p-value <1.13e-05) on chromosomes 1, 2, 4, 15, and 19. Significant markers were associated with genes notable for relevant wool biological functions, including the gene ABCC8 which codes for SUR1, an ATP-sensitive potassium channel known to affect hair growth and 60S ribosomal protein L17-like, previously found to be expressed during follicle formation. The strongest Pearson correlation coefficients were identified between clean fleece wt. 365 adj. and grease fleece wt. 365 adj. (r = 0.83) and between clean fleece wt. 365 adj. and staple length 365 adj. (r = 0.53). Additionally, clean fleece wt. 365 adj. was correlated with final body weight (r = 0.35) and scrotal circumference (r = 0.16). Staple length 365 adj. (p-value = 5e-04), average fiber diameter (p-value = .0053) and clean fleece wt. 365 adj. (p-value = .014) were significantly associated with belly wool score. Discussion: The results of this study provide important insight into the relationships between wool quality characteristics and report specific markers that Rambouillet sheep producers may use to help inform selection and breeding decisions for improved wool quality.

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Platinum-Quality Mitogenome Haplotypes from United States Populations.

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Platinum-Quality Mitogenome Haplotypes from United States Populations.

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