Population-specific Reference Research Articles

The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs

Pigs play a central role in human livelihoods in China, but a lack of systematic large-scale whole-genome sequencing of Chinese domestic pigs has hindered genetic studies. Here, we present the 1000 Chinese Indigenous Pig Genomes Project sequencing dataset, comprising 1011 indigenous individuals from 50 pig populations covering approximately two-thirds of China’s administrative divisions. Based on the deep sequencing (~25.95×) of these pigs, we identify 63.62 million genomic variants, and provide a population-specific reference panel to improve the imputation performance of Chinese domestic pig populations. Using a combination of methods, we detect an ancient admixture event related to a human immigration climax in the 13th century, which may have contributed to the formation of southeast-central Chinese pig populations. Analyzing the haplotypes of the Y chromosome shows that the indigenous populations residing around the Taihu Lake Basin exhibit a unique haplotype. Furthermore, we find a 13 kb region in the THSD7A gene that may relate to high-altitude adaptation, and a 0.47 Mb region on chromosome 7 that is significantly associated with body size traits. These results highlight the value of our genomic resource in facilitating genomic architecture and complex traits studies in pigs.

Normal Gut Microbiomes in Diverse Populations: Clinical Implications.

The human microbiome is a sensor and modulator of physiology and homeostasis. Remarkable tractability underpins the promise of therapeutic manipulation of the microbiome. However, the definition of a normal or healthy microbiome has been elusive. This is in part due to the underrepresentation of minority groups and major global regions in microbiome studies to date. We review studies of the microbiome in different populations and highlight a commonality among health-associated microbiome signatures along with major drivers of variation. We also provide an overview of microbiome-associated therapeutic interventions for some widespread, widely studied diseases. We discuss sources of bias and the challenges associated with defining population-specific microbiome reference bases. We propose a roadmap for defining normal microbiome references that can be used for population-customized microbiome therapeutics and diagnostics.

Comparison of fetal growth patterns from Western India with Intergrowth-21st.

To generate longitudinal fetal growth data in an Indian population and compare it with Intergrowth-21st. Fetal biometry data was collected in a prospective longitudinal observational study (REVAMP: Research Exploring Various Aspects and Mechanisms in Preeclampsia) from 2017 to 2022. Fetal crown-rump length (CRL) was measured at 11-14 weeks gestation, and biparietal diameter (BPD), head circumference (HC), abdominal circumference (AC), and femur length (FL) at 18-22 and 32-35 weeks, and converted into Z-scores using the Intergrowth standard. Generalized Additive Models for Location, Scale and Shape (GAMLSS) models were used to construct fetal growth centile curves compared against Intergrowth centiles. Out of 1096 singleton pregnancies in REVAMP, this analysis included 655 'healthy' pregnancies (uncomplicated by pre-eclampsia, diabetes, pre-term delivery or low birth weight) and a sub-set of 106 'low-risk' pregnancies defined using Intergrowth criteria. The 'healthy' study subjects showed lower mean CRL Z-score [-0.45 SD (95% CI:-0.54,-0.37)] at 11-14 weeks, and BPD Z-score [-1.2 SD (-1.28,-1.11) and -1.17 SD (-1.23,-1.1)] at 18-22 and 32-35 weeks respectively. Mean HC Z-score was comparable to the Intergrowth standard at 18-22 weeks [-0.08 SD (-0.16, 0.02)] but smaller at 32-35 weeks [-0.25 SD (-0.32,-0.19)]. Mean AC Z-score was lower at 18-22 weeks [-0.32 SD (-0.41,-0.23)] but comparable at 32-35 weeks [0.004 SD (-0.07, 0.07)]. FL was comparable to or larger than the Intergrowth standard at both time points [0.05 SD (-0.05, 0.14); 0.82 SD (0.75, 0.89), respectively]. These findings were similar, though measurements were slightly larger, in the 'low-risk' sample. This data from healthy and low-risk pregnant women in urban western India indicates that some fetal dimensions and growth trajectories differ significantly from the Intergrowth-21st. Our data suggest the need for a larger representative study to define a population-specific fetal growth reference for India, for identification of fetal growth restriction.

Anthropometric indices growth references (length, Weight and Head Circumferences) of children aged 0–24 months in North-East of Iran by GAMLSS

BackgroundGrowth references play a crucial role in the screening, evaluation, and surveillance of children, aiding in the early identification of the requirement for diverse growth-promoting interventions. Variations in human growth across distinct ethnic cohorts arise from genetic disparities, lifestyle variances, nutritional diversity, and diverse social and environmental contexts. Consequently, the selection of growth references markedly influences the prevalence of developmental disorders and nutritional imbalances in children. The study aims to assess the growth percentile of children in the north-east of Iran and establish population-specific reference charts for length, weight, and head circumference spanning from birth to 24 months.MethodsThis cross-sectional population-based research conducted in the north-east of Iran, from 2016 to 2023. The Data extracted from the electronic health records of Mashhad University of Medical Sciences. All apparently healthy children aged from birth to 24 months who were measured at least once by health staff at the ages of birth,1,2,4,6,7,9,12,15,18,24 months were included. The target population of the study were 479,089 children (96.21%), encompassing 233,565 girls (48.75%) and 245,524 boys (51.25%). Gender-specific percentile curves for length, weight, and head circumference concerning age, as well as weight concerning length, were derived using the GAMLSS approach.ResultsFrom the anthropometric information of 479,089 children (245,524 boys and 233,565 girls), growth charts were constructed. In comparison to the standard WHO chart, Iranian neonates displayed lower weight across all percentiles during the first month after birth, exhibited decreased head circumference at the 3rd percentile, and boys showed reduced length across all percentiles. After this age, Iranian children demonstrated increased weight, length, and head circumference.ConclusionsThis research introduces the inaugural large-scale endeavor for indigenous reference charts. Through the noted distinctions from the international reference, the utilization of this novel resource offers the potential to enhance the surveillance of children’s growth within the area. Moreover, by accurately assessing growth anomalies such as underweight, stunting, and wasting, it expands the domain of impactful policies in this sphere. Simultaneously, it enables the exploration of the secular trend of children’s growth in the forthcoming years.

Enhancing Variant Calling in Whole-Exome Sequencing Data Using Population-Matched Reference Genomes.

Whole-exome sequencing (WES) data are frequently used for cancer diagnosis and genome-wide association studies (GWAS), based on high-coverage read mapping, informative variant calling, and high-quality reference genomes. The center position of the currently used genome assembly, GRCh38, is now challenged by two newly published telomere-to-telomere (T2T) genomes, T2T-CHM13 and T2T-YAO, and it becomes urgent to have a comparative study to test population specificity using the three reference genomes based on real case WES data. Here we report our analysis along this line for 19 tumor samples collected from Chinese patients. The primary comparison of the exon regions among the three references reveals that the sequences in up to ∼ 1% target regions in T2T-YAO are widely diversified from GRCh38 and may lead to off-target in sequence capture. However, T2T-YAO still outperforms GRCh38 genomes by obtaining 7.41% more mapped reads. Due to more reliable read-mapping and closer phylogenetic relationship with the samples than GRCh38, T2T-YAO reduces half of variant calls of clinical significance which are mostly benign, while maintaining sensitivity in identifying pathogenic variants. T2T-YAO also outperforms T2T-CHM13 in reducing calls of Chinese-specific variants. Our findings highlight the critical need for employing population-specific reference genomes in genomic analysis to ensure accurate variant analysis and the significant benefits of tailoring these approaches to the unique genetic backgrounds of each ethnic group.

A-050 Reference Intervals for Plasma Concentrations of C-Terminal Telopeptide of Type-I Collagen (CTX) for Greek Adult Population

Abstract Background CTX assays measure a fragment of the C-terminal telopeptide of type I collagen released during resorption of mature bone. To adequately interpret CTX results, method-specific and population specific reference intervals are needed. We aimed to determine reference intervals for plasma concentrations of CTX. Methods We collected samples from 431 apparently healthy Greeks (140 men as well as 150 pre- and 139 postmenopausal women), who volunteered to participate in our study. Data on socio-demographic characteristics, medical histories and medications were collected and subjects with conditions or receiving medications that affecting bone metabolism were excluded. Dual-energy x-ray absorptiometry (DXA) used to measure bone mineral density (BMD) in all participants. All blood collections were performed in the morning after overnight fast. Plasma EDTA samples were used for the measurement of CTX. Measurements were performed by an automated chemiluminescent immunoassay on the Maglumi-X3 analyzer (Snibe, Shenzhen, China). The reference interval was defined as the central 95% range and determined according to CLSI guide C28-A3 using the MedCalc Software. Results The table summarizes our results. The mean age of men, pre- and post-menopausal women were 50.7, 40,7 and 58.4 years respectively. DXA results revealed that 348 participants had normal BMD, 74 HAD osteopenia and 9 had osteoporosis which excluded from analysis. Since our data were not normally distributed (Shapiro-Wilk test) in any group and after the exclusion of outliers (Tukey test), we used the non-parametric method suggested by the CLSI guide to determine the reference intervals. Multiple regression analysis also revealed that sex menopausal status and BMD were factors affecting CTX values. Conclusions We provide reference intervals for the determination of CTX concentrations in EDTA-plasma for the Greek adult population using an automated immunoassay. Our data may aid to interpret bone turnover in the Greek adult population.

A-112 Reference Intervals for Serum Concentrations of N-Terminal Propeptide of Type-I Procollagen (PINP) for Greek Adult Population

Abstract Background PINP is a sensitive indicator of the synthesis of type-I collagen. Serum PINP levels are affected by changes in bone metabolism and is a useful indicator of disease activity in Paget's disease, bone metastases of osteoblastic nature and in monitoring osteoporosis treatment. To interpret PINP, method and population specific reference intervals are needed. We aimed to determine reference intervals for serum concentrations of PINP for the Greek adult population. Methods We collected samples from 431 apparently healthy Greeks (140 men as well as 150 pre- and 139 post-menopausal women), who volunteered to participate in our study. Data on socio-demographic characteristics, medical histories and medications were collected and subjects with conditions or receiving medications that affecting bone metabolism were excluded. Dual-energy x-ray absorptiometry (DXA) used to measure bone mineral density (BMD) in all participants. All blood collections were performed in the morning after overnight fast. Measurements were performed by an automated chemiluminescent immunoassay on the Maglumi-X3 analyzer (Snibe, Shenzhen, China). This method measures the total-PINP in serum. The reference interval was defined as the central 95% range and determined according to CLSI guide C28-A3 using the MedCalc Software Results The table summarizes our results. DXA results revealed that 348 participants had normal BMD, 74 had osteopenia and 9 had osteoporosis which excluded from analysis. Since our data were not normally distributed (Shapiro-Wilk test) in any group and after the exclusion of outliers (Tukey test), we used the non-parametric method suggested by the CLSI guide in order to determine the reference intervals. Multiple regression analysis revealed that sex and menopausal status were factors affecting PINP values. Conclusions We provide reference intervals for the determination of PINP concentrations in serum for the Greek adult population using an automated immunoassay. Our data may aid to interpret bone turnover in the Greek adult population.

Trimester-Specific Free Thyroid Hormones Levels among Pregnant Women in Nineveh Governorate,Iraq

AbstractThere are numerous physiological changes in thyroid gland functions occur during conception that lead to differ in thyroid hormones levels. Therefore, American Thyroid Association (ATA) guidelines recommended determination of population specific reference serum levels for thyroid hormones in different trimesters. Aim of current study is to establish trimester –specific reference serum levels (TSRSLs) for free triiodothyronine (FT3) and free thyroxine (FT4) in apparently healthy pregnant females in Nineveh governorate, Iraq.Accordingly, a cross-sectional study was carried out from Dec. 2020 to Apr. 2021 in Al-Batool Teaching hospital, Al-khanssa Maternity Teaching Hospital, Al-Noor Primary Health Center (PHC) and Out- patient clinics in Nineveh governorate. A total of 300 pregnant women were enrolled in this study after obtaining oral and written consent, 140 were excluded since they were met one or more of exclusion criteria, other 10 found to be positive anti-thyroid peroxide were also excluded from the study. The remaining 150 pregnant females aged (16-42) years were enrolled in this study, 50 of them were assigned to each trimester.The following parameters FT4 and FT3 were measured for each participants. The result of this study showed the TSRSLs of FT4 were (0.70-1.29, 0.49-1.31 and 0.58-1.28 ng/dl) for the 1st, 2nd and 3rd trim, respectively and for FT3 were ( 2.63-3.96, 2.04-3.3 and 2.11-3.40 pg/ml) for the 1st, 2nd and 3rd trim, respectively. The mean FT4 and FT3 was significantly decreased (P=0.002 and P<0.0001), respectively. from 1st to 3rd trim. The current study are reported the TSRSLs of FT3 and FT4 for the first time in Nineveh governorate. We concluded nearly similar TSRSLs of FT3 and FT4 to that recorded elsewhere

Harnessing the Power of Big Data Analytics-Estimation of Reference Intervals for Neonatal Serum TSH in Pakistan Using RefineR Algorithm.

To estimate the population-specific reference intervals (RIs) for neonatal thyroid stimulating hormone (TSH) in Pakistani neonates, utilising the refineR algorithm. Observational study. Place and Duration of the Study: Department of Pathology and Laboratory Medicine, The Aga Khan University Hospital, Karachi, Pakistan, from 17th May to 30th November 2023. A data mining analysis was conducted on serum TSH results of neonates (≤1 month) over a period of six years, following approval from the Institutional Ethical Review Committee. Two subgroups were assessed based on the age as 0 - 5 days and 6 - 30 days. The refineR algorithm was implemented using refineR package (version 1.0.0), ensuring accurate analysis and insights. A total of non-duplicate 82,299 neonatal serum TSH tests were retrieved, including 70,788 (88%) aged 0 - 5 days and 11,511 (12%) aged ranging from 6 - 30 days. The estimated RI was from 0.67 µIU/mL (90% CI 0.641 - 0.72) to 15.0 µIU/mL (90% CI 13.2 - 17.3) for the first age group and 0.65 µIU/mL (90% CI 0.6 - 0.84) to 8.6 µIU/mL (90% CI 8.05 - 9.71) for the second age group. Reference intervals for neonatal serum TSH of the Pakistani population were estimated, considering the genetic differences of this demographic in comparison to the Western population. Results aligned with global literature, validating the refineR indirect approach's applicability. Reference intervals, Neonatal, Thyroid stimulating hormone, RefineR algorithm, Big data, Pakistan.

Cord Blood Proteomic Profiles, Birth Weight, and Early Life Growth Trajectories

The cord blood proteome, a repository of proteins derived from both mother and fetus, might offer valuable insights into the physiological and pathological state of the fetus. However, its association with birth weight and growth trajectories early in life remains unexplored. To identify cord blood proteins associated with birth weight and the birth weight ratio (BWR) and to evaluate the associations of these cord blood proteins with early growth trajectories. This cohort study included 288 mother-child pairs from the ongoing prospective Environmental Influence on Early Aging birth cohort study. Newborns were recruited from East-Limburg Hospital in Genk, Belgium, between February 2010 and November 2017 and followed up until ages 4 to 6 years. Data were analyzed from February 2022 to September 2023. The outcome of interest was the associations of 368 inflammatory-related cord blood proteins with birth weight or BWR and with early life growth trajectories (ie, rapid growth at age 12 months and weight, body mass index [BMI] z score, waist circumference, and overweight at age 4-6 years) using multiple linear regression models. The BWR was calculated by dividing the birth weight by the median birth weight of the population-specific reference growth curve, considering parity, sex, and gestational age. Results are presented as estimates or odds ratios (ORs) for each doubling in proteins. The sample included 288 infants (125 [43.4%] male; mean [SD] gestation age, 277.2 [11.6] days). The mean (SD) age of the child at the follow-up examination was 4.6 (0.4) years old. After multiple testing correction, there were significant associations of birth weight and BWR with 7 proteins: 2 positive associations: afamin (birth weight: coefficient, 341.16 [95% CI, 192.76 to 489.50]) and secreted frizzled-related protein 4 (SFRP4; birth weight: coefficient, 242.60 [95% CI, 142.77 to 342.43]; BWR: coefficient, 0.07 [95% CI, 0.04 to 0.10]) and 5 negative associations: cadherin EGF LAG 7-pass G-type receptor 2 (CELSR2; birth weight: coefficient, -237.52 [95% CI, -343.15 to -131.89]), ephrin type-A receptor 4 (EPHA4; birth weight: coefficient, -342.78 [95% CI, -463.10 to -222.47]; BWR: coefficient, -0.11 [95% CI, -0.14 to -0.07]), SLIT and NTRK-like protein 1 (SLITRK1; birth weight: coefficient, -366.32 [95% CI, -476.66 to -255.97]; BWR: coefficient, -0.11 [95% CI, -0.15 to -0.08]), transcobalamin-1 (TCN1; birth weight: coefficient, -208.75 [95% CI, -305.23 to -112.26]), and unc-5 netrin receptor D (UNC5D; birth weight: coefficient, -209.27 [95% CI, -295.14 to -123.40]; BWR: coefficient, -0.07 [95% CI, -0.09 to -0.04]). Further evaluation showed that 2 proteins were still associated with rapid growth at age 12 months (afamin: OR, 0.32 [95% CI, 0.11-0.88]; TCN1: OR, 2.44 [95% CI, 1.26-4.80]). At age 4 to 6 years, CELSR2, EPHA4, SLITRK1, and UNC5D were negatively associated with weight (coefficients, -1.33 to -0.68 kg) and body mass index z score (coefficients, -0.41 to -0.23), and EPHA4, SLITRK1, and UNC5D were negatively associated with waist circumference (coefficients, -1.98 to -0.87 cm). At ages 4 to 6 years, afamin (OR, 0.19 [95% CI, 0.05-0.70]) and SLITRK1 (OR, 0.32 [95% CI, 0.10-0.99]) were associated with lower odds for overweight. This cohort study found 7 cord blood proteins associated with birth weight and growth trajectories early in life. Overall, these findings suggest that stressors that could affect the cord blood proteome during pregnancy might have long-lasting associations with weight and body anthropometrics.

Establishment of dry-chemistry-based reference intervals of routine liver function tests for the adult population of Gandaki Province, Nepal.

Every clinical laboratory should ideally establish its own population-specific reference intervals (RIs) to promote precision and evidence-based medicine. However, clinical laboratories in Nepal find it easier to follow external RIs than establish their own, leading to a lack of RIs specific to the local population. This study thus aimed to establish RIs of routine LFTs for the adult population of Gandaki Province, Nepal, and compare them with the current RIs used by our laboratory. We established the dry-chemistry-based reference intervals of 11 common LFT parameters for the adult population of Gandaki Province, Nepal using the direct priori-based method. The combined and sex-specific 95% double-sided RIs of total protein, albumin, globulin, A/G ratio, bilirubin, aspartate aminotransaminase (AST), alanine aminotransaminase (ALT), AST/ALT ratio, and alkaline phosphatase (ALP) were established using non-parametric percentile method. The new RIs were also compared with the currently used RIs that were adopted from the reagent kit inserts. The newly established RIs for each LFT were: Total proteins: 68.0-69.0g/L, albumin: 39.0-52.0g/L; globulin: 27.0-42.0g/L; A/G ratio: 1.1-1.8; total bilirubin: 5.13-25.65μmol/L (0.30-1.50mg/dl); unconjugated bilirubin: 1.71-17.10μmol/L (0.10-1.00mg/dl); conjugated bilirubin: 0.00-10.26 μmol/L (0.00-0.60mg/dl); AST: 20.0-43.2U/L; ALT: 11.0-53.0 U/L; AST/ALT ratio: 0.7-2.1; ALP: 42.0-135.4U/L. The RIs of albumin, globulin, A/G ratio, AST, ALT, and AST/ALT ratio differed significantly (p < 0.05) between males and females. Moreover, calculated out-of-range values showed that up to 4-40% of apparently healthy adults were classified as having abnormal test results based on current RIs. The newly established RIs fulfil the need for population and platform-specific RIs for the adult population of Gandaki Province of Nepal and bring more conformity and accuracy in interpreting the LFT results, diagnosis of hepatobiliary diseases, clinical decision-making, monitoring the success of therapy and future liver specific biomedical researches within the Gandaki Province of Nepal.

DANSPOT: A Multicenter Stepped-Wedge Cluster-Randomized Trial of the Reclassification of Acute Myocardial Infarction: Rationale and Study Design.

Cardiac troponins are the preferred biomarkers for the diagnosis of acute myocardial infarction. Although sex-specific 99th percentile thresholds of troponins are recommended in international guidelines, the clinical effect of their use is poorly investigated. The DANSPOT Study (The Danish Study of Sex- and Population-Specific 99th percentile upper reference limits of Troponin) aims to evaluate the clinical effect of a prospective implementation of population- and sex-specific diagnostic thresholds of troponins into clinical practice. This study is a nationwide, multicenter, stepped-wedge cluster-randomized trial of the implementation of population- and sex-specific thresholds of troponins in 22 of 23 clinical centers in Denmark. We established sex-specific thresholds for 5 different troponin assays based on troponin levels in a healthy Danish reference population. Centers will sequentially cross over from current uniform manufacturer-derived thresholds to the new population- and sex-specific thresholds. The primary cohort is defined as patients with symptoms suggestive of acute coronary syndrome having at least 1 troponin measurement performed within 24 hours of arrival with a peak troponin value between the current uniform threshold and the new sex-specific female and male thresholds. The study will compare the occurrence of the primary outcome, defined as a composite of nonfatal myocardial infarction, unplanned revascularization, and all-cause mortality within 1 year, separately for men and women before and after the implementation of the new sex-specific thresholds. The DANSPOT Study is expected to show the clinical effects on diagnostics, treatment, and clinical outcomes in patients with myocardial infarction of implementing sex-specific diagnostic thresholds for troponin based on a national Danish reference population. URL: https://www.clinicaltrials.gov; Unique identifier: NCT05336435.

Phenomic landscape and pharmacogenomic implications for HLA region in a Taiwan Han Chinese population

BackgroundThe human leukocyte antigen (HLA) genes, exhibiting significant genetic diversity, are associated with susceptibility to various clinical diseases and diverse in drug responses. High costs of HLA sequencing and the population-specific architecture of this genetic region necessitate the establishment of a population-specific HLA imputation reference panel. Moreover, there is a lack of understanding about the genetic and phenotypic landscape of HLA variations within the Taiwanese population.MethodsWe created models for a Taiwanese-specific HLA imputation reference panel. These models were trained with the array genotype data and HLA sequencing data from 845 Taiwanese subjects. HLA imputation was applied for 59,448 Taiwanese subjects to characterize the HLA allele and haplotype frequencies. Additionally, a phenome-wide association study (PheWAS) was conducted to identify the phenotypes associated with HLA variations. The association of the biallelic HLA variants with the binary and quantitative traits were evaluated with additive logistic and linear regression models, respectively. Furthermore, an omnibus test with likelihood-ratio test was applied for each HLA amino acid position in the multiallelic HLA amino acid polymorphisms to compare the difference between a fitted model and a null model following a χ2 distribution of n-1 degree of freedom at a position with n residues. Finally, we estimated the prevalence of adverse drug reactions (ADR)-related HLA alleles in the Taiwanese population.ResultsIn this study, the reference panel models displayed remarkable accuracy, with averages of 99.3%, 98.9%, and 99.1% for 2-, 4-, 6-digit alleles of the eight classical HLA genes, respectively. For PheWAS, a total of 18,136 significant associations with HLA variants across 26 phenotypes are identified (p < 5×10-8), highlighting the pleiotropy feature of the HLA region. Among the independent signals, 15 are novel, including the association of HLA-B pos 138 variation with ankylosing spondylitis (AS), and rs9266290 and rs9266292 with allergy. Through an analysis spanning the entire HLA region, we identified clusters of phenotype correlations. Finally, the carriers of pharmacogenomic related HLA alleles, including HLA-C*01:02 (35.86%), HLA-B*58:01 (20.9%), and HLA-B*15:02 (8.38%), were characterized in the Taiwanese general population.ConclusionsWe successfully delivered the HLA imputation for 59,448 Taiwanese subjects and characterized the genetic and phenotypic landscapes of the HLA variations. In addition, we quantified the estimated prevalence of the ADR-related HLA alleles in the Taiwanese population. The developed HLA imputation reference panel could be used for estimation of population HLA allele frequencies, which can facilitate further studies in the role of HLA variants in a wider range of phenotypes in the population.

Establishing population-specific reference intervals for AMH & enhancing its use as a diagnostic marker in PCOS

Establishing population-specific reference intervals for AMH & enhancing its use as a diagnostic marker in PCOS

Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil

BackgroundThe final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics).ResultsThe analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response.ConclusionsThe predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils.7k5euw-hvBknz_jds4sXXfVideo

Next-generation sequencing analysis with a population-specific human reference genome.

Next-generation sequencing (NGS) has become widely available and is routinely used in basic research and clinical practice. The reference genome sequence is an essential resource for NGS analysis, and several population-specific reference genomes have recently been constructed to provide a choice to deal with the vast genetic diversity of human samples. However, resources supporting population-specific references are insufficient, and it is burdensome to perform analysis using these reference genomes. Here, we constructed a set of resources to support NGS analysis using the Japanese reference genome, JG. We created resources for variant calling, variant-effect prediction, gene and repeat element annotations, read mappability, and RNA-seq analysis. We also provide a resource for reference coordinate conversion for further annotation enrichment. We then provide a variant calling protocol with JG. Our resources provide a guide to prepare sufficient resources for the use of population-specific reference genomes and can facilitate the migration of reference genomes.

A national data sharing solution for the prevention and treatment of obesity-a qualitative study of stakeholders' needs.

Obesity-related health data is needed for studies and precision medicine, but existing registers, medical chart systems, and digital platforms are seldom compatible. Before creating improved ways of sharing health data, this study aimed to gather opinions, experiences, and wishes from stakeholders that may use obesity-related health data: healthcare, researchers, people with overweight or obesity, the pharmaceutical industry, and IT-specialists. We performed semistructured interviews with 28 stakeholders and analyzed qualitative text data with inductive content analysis. We grouped the suggested parameters in categories. Time efficient data entering was perceived crucial. Access to health data was important to all participants. Some parameters, such as age, BMI, and sex were requested by all stakeholders. Other data were stakeholder specific, such as population-specific laboratory references, suggested by healthcare professionals only. For people with overweight or obesity, ability to share data with healthcare staff about fitness level or previous weight loss attempts, was important. The results from this study can be used in the design and implementation of a national health data sharing solution that may be used for precision healthcare use and to evaluate and guide obesity treatment and preventive measures. Data parameters requested by all populations, such as BMI, sex, and age, should be prioritized when designing a data solution. Ability for individuals with overweight or obesity to share health data, may improve healthcare appointments and reduce weight stigma.

Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.

Large-scale imputation reference panels are currently available and have contributed to efficient genome-wide association studies through genotype imputation. However, whether large-size multi-ancestry or small-size population-specific reference panels are the optimal choices for under-represented populations continues to be debated. We imputed genotypes of East Asian (180k Japanese) subjects using the Trans-Omics for Precision Medicine reference panel and found that the standard imputation quality metric (Rsq) overestimated dosage r2 (squared correlation between imputed dosage and true genotype) particularly in marginal-quality bins. Variance component analysis of Rsq revealed that the increased imputed-genotype certainty (dosages closer to 0, 1 or 2) caused upward bias, indicating some systemic bias in the imputation. Through systematic simulations using different template switching rates (θvalue) in the hidden Markov model, we revealed that the lower θ value increased the imputed-genotype certainty and Rsq; however, dosage r2 was insensitive to the θ value, thereby causing a deviation. In simulated reference panels with different sizes and ancestral diversities, the θ value estimates from Minimac decreased with the size of a single ancestry and increased with the ancestral diversity. Thus, Rsq could be deviated from dosage r2 for a subpopulation in the multi-ancestry panel, and the deviation represents different imputed-dosage distributions. Finally, despite the impact of the θ value, distant ancestries in the reference panel contributed only a few additional variants passing a predefined Rsq threshold. We conclude that the θ value substantially impacts the imputed dosage and the imputation quality metric value.

Identification of OPTN p.(Asn51Thr): A novel pathogenic variant in primary open-angle glaucoma

PurposePathogenic variants in TBK1, MYOC, and OPTN are associated with primary open-angle glaucoma (POAG) with severe visual field defects. This study aims to understand further POAG-related pathogenic variant(s) based on a cohort of East Asian populations that have not been well-characterized. MethodsWe conducted a comprehensive screening of TBK1, MYOC, and OPTN variants in 174 POAG Japanese patients, followed by 8380 population-specific genome sequencing data references, segregation analysis, and functional protein assays to determine pathogenic variants. ResultsDespite the small sample size, 4 variants were novel, 2 of which p.(Cys5Trp) and p.(Thr293Met) were in the MYOC gene, and 2 p.(Asn51Thr), and p.(Gln142His) were in the OPTN. Notably, the OPTN p.(Asn51Thr) missense variant adjacent to the p.(Glu50Lys) variant, a well-known POAG pathogenic variant, was segregated from all proband’s family members with POAG. Moreover, in silico and in vitro analyses revealed that the OPTN p.(Asn51Thr) protein increased binding instability, interactions of the OPTN-TBK1 complex, and enhanced protein insolubility, likewise the p.(Glu50Lys) protein. ConclusionOur findings may provide further genetic insights into rare variants of POAG and support the clear conclusion that OPTN p.(Asn51Thr) is a novel likely pathogenic variant.

Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation.

Despite rapid improvements in the accessibility of whole-genome sequencing (WGS), understanding the extent of human genetic variation is limited by the scarce availability of genome sequences from underrepresented populations. Developing the population-scale reference database of Latvian genetic variation may fill the gap in European genomes and improve human genomics research. In this study, we analysed a high-coverage WGS dataset comprising 502 individuals selected from the Genome Database of the Latvian Population. An assessment of variant type, location in the genome, function, medical relevance, and novelty was performed, and a population-specific imputation reference panel (IRP) was developed. We identified more than 18.2 million variants in total, of which 3.3% so far are not represented in gnomAD and dbSNP databases. Moreover, we observed a notable though distinct clustering of the Latvian cohort within the European subpopulations. Finally, our findings demonstrate the improved performance of imputation of variants using the Latvian population-specific reference panel in the Latvian population compared to established IRPs. In summary, our study provides the first WGS data for a regional reference genome that will serve as a resource for the development of precision medicine and complement the global genome dataset, improving the understanding of human genetic variation.