Biology subjects

Mao, S.

Publications and source records attributed to Mao, S..

60 records · Page 4Linked to original sources

bioRxiv2019

Genome-Wide Polygenic Risk Scores and prediction of Gestational Diabetes in South Asian Women

Gestational diabetes Mellitus (GDM) affects 1 in 7 births and is associated with numerous adverse health outcomes for both mother and child. GDM is suspected to share a large common genetic background with type 2 diabetes (T2D). The first aim of this study, was to characterize different GDM polygenic risk scores (PRSs) using data from the South Asian Birth Cohort (START). The second aim of this study was to estimate the heritability of GDM.\n\nPRSs were derived for 832 South Asian women from START using the pruning and thresholding (P+T), LDpred, and GraBLD methods. Weights were derived from multi-ethnic (Mahajan et al., 2014) and white Caucasian (Scott et al., 2017) studies of the DIAGRAM consortium. Association with GDM was tested using logistic regression. Heritability of GDM was estimated using the GRMEL approach. Results were replicated in samples from the UK Biobank (UKB) study.\n\nThe top P+T, LDpred and GraBLD PRSs were all based on Mahajan et al. The best PRS was highly associated with GDM in START (AUC=0.62, OR=1.60 [95% CI=1.44-1.69]), and in South Asian (AUC=0.65) and white British (AUC=0.58) women from UKB. Heritability of GDM approximated 0.55{+/-}0.83 in START and 0.18{+/-}0.22 in white British women from UKB.\n\nOur results highlight the importance of combining genome-wide genotypes and summary statistics from large multi-ethnic studies to optimize PRSs in South Asians.

genomics↗

bioRxiv2019

Perinatal features of Prader-Willi syndrome: a Chinese cohort

BackgroundPrader-Willi syndrome (PWS) is a rare complex genetic disorder caused by an absence of expression of imprinted genes on the paternally derived chromosome 15q11-q13 region. This study aimed to characterize the perinatal features in a cohort of Chinese individuals with PWS.\n\nMethodsWe analyzed anonymous data of 134 patients from the PWS Registry in China. Perinatal and neonatal presentations were analyzed, and compared between the two PWS genetic subtypes. We also compared the perinatal features of PWS patients with the general population and other previous reported large cohorts from France, UK and USA.\n\nResultsThis study included 134 patients with PWS (115 patients with 15q11-q13 deletion and 19 with maternal UPD). High mean maternal age was found in this cohort (30.5 vs. 26.7) comparing with the general population. 88.6% of mothers reported a decrease of fetal movements. 42.5% and 18.7% of mothers had polyhydramnios and oligohydramnios during pregnancy, respectively. 82.8% of the patients were born by caesarean section. 32.1% of neonates had birth asphyxia, 98.5% had hypotonia and 97.8% had weak cry or even no cry at neonatal period. Feeding difficulty existed in 99.3% of the infants, and 94.8% of them had failure to thrive. 69.4% of the infants ever used feeding tube during hospitalization. However, 97.8% of them discontinued tube feeding after discharged home. Maternal age, maternal pre-pregnancy weight and BMI were significantly higher in the UPD group (all P<0.05).\n\nConclusionsPWS should be highlighted for differential diagnosis for infants with following perinatal factors including polyhydramnios, intrauterine decreased fetal movements, cesarean section, low birth weight, feeding difficulty, hypotonia, and failure to thrive. Higher maternal age may be a risk factor for PWS, especially for UPD, and further studies for the mechanism of PWS are required.\n\nAuthor SummaryEarly diagnosis and tailored multidisciplinary treatment are utmost important for better quality of life of the infants with Prader-willi syndrome. Genetic diagnosis for PWS is now easily available; and diagnosis can be made in most patients within the first months of life even prenatally if obstetricians or neonatologists can recognize the perinatal features of PWS well. However, most patients still had a late diagnosis because the early signs of PWS not recognized. Our study highlighted the perinatal features of a large cohort of Chinese patients with PWS, which will benefit for early diagnosis and treatment. We found high incidence of decreased fetal movements, polyhydramnios and delivery by cesarean section, and higher maternal age comparing with the general population. Neonatal features found in our cohort included low birth weight, birth asphyxia, failure to thrive, feeding difficulty, weak cry and hypotonia. We found mothers with UPD had higher maternal age, pre-pregnancy weight and BMI. Most patients required tube feeding during hospitalization, however tube feeding was discontinued by their parents after discharge at home. Nutrition deficiency was a serious problem in infants with PWS. Home tube-feeding instruction should be carried out for parents of PWS patients in China.

genetics↗

bioRxiv2018

A study of analytical strategies to include X-chromosome in variance heterogeneity analysis: evidence for trait-specific polygenic variance structure

Genotype-stratified variance of a quantitative trait could differ in the presence of gene-gene or gene-environment interactions. Genetic markers associated with phenotypic variance are thus considered promising candidates for follow-up interaction or joint location-scale analyses. However, as in studies of main effects, the X-chromosome is routinely excluded from whole-genome scans due to analytical challenges. Specifically, as males carry only one copy of the X-chromosome, the inherent sex-genotype dependency could bias the trait-genotype association, through sexual dimorphism in quantitative traits with sex-specific means or variances. Here we investigate phenotypic variance heterogeneity associated with X-chromosome SNPs and propose valid and powerful strategies. Among those, a generalized Levenes test has adequate power and remains robust to sexual dimorphism. An alternative approach is sex-stratified analysis but at the cost of slightly reduced power and modeling flexibility. We applied both methods to an Estonian study of gene expression quantitative trait loci (eQTL; n=841), and two complex trait studies of height, hip and waist circumferences, and body mass index from multi-ethnic study of atherosclerosis (MESA; n=2,073) and UK Biobank (UKB; n=327,393). Consistent with previous eQTL findings on mean, we found some but no conclusive evidence for cis regulators being enriched for variance association. SNP rs2681646 is associated with variance of waist circumference (p=9.5E-07) at X-chromosome-wide significance in UKB, with a suggestive female-specific effect in MESA (p=0.048). Collectively, an enrichment analysis using permutated UKB (p<1/10) and MESA (p<1/100) datasets, suggests a possible polygenic structure for the variance of human height.

genetics↗

bioRxiv2017

Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. We determined gastrointestinal colonisation prevalence of ESC-resistant E. coli (ESC-R-EC) and K. pneumoniae (ESC-R-KP) in Cambodian children/adolescents and associated risk factors; characterised relevant resistance genes, their genetic contexts, and the genetic relatedness of ESC-R strains using whole genome sequencing (WGS). Faeces and questionnaire data were obtained from individuals <16 years in northwestern Cambodia, 2012. WGS of cultured ESC-R-EC/KP was performed (Illumina). Maximum likelihood phylogenies were used to characterise relatedness of isolates; ESC-R-associated resistance genes and their genetic contexts were identified from de novo assemblies using BLASTn and automated/manual annotation. 82/148 (55%) of children/adolescents were ESC-R-EC/KP colonised; 12/148 (8%) were co-colonised with both species. Independent risk factors for colonisation were hospitalisation (OR: 3.12, 95%, CI [1.52-6.38]) and intestinal parasites (OR: 3.11 [1.29-7.51]); school attendance conferred decreased risk (OR: 0.44 [0.21-0.92]. ESC-R strains were diverse; the commonest ESC-R mechanisms were blaCTX-M 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for blaCTX-M-15, -55 and -27, frequently involved IS26. Chromosomal blaCTX-M integration was common in E. coli. Gastrointestinal ESC-R-EC/KP colonisation is widespread in Cambodian children/adolescents; hospital admission and intestinal parasites are independent risk factors. The genetic contexts of blaCTX-M are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of blaCTX-M may result in stable propagation in these community-associated pathogens.

microbiology↗

bioRxiv2017

Regional Polygenic Covariance Reveals Heterogeneity In The Shared Heritability Between Complex Traits

BackgroundComplex traits can share a substantial proportion of their polygenic heritability. However, genome-wide polygenic correlations between pairs of traits can mask heterogeneity in their shared polygenic effects across loci. We propose a novel method (WML-RPC) to evaluate polygenic correlation between two complex traits in small genomic regions using summary association statistics. Our method tests for evidence that the polygenic effect at a given region affects two traits concurrently.\n\nResultsWe show through simulations that our method is well calibrated, powerful and more robust to misspecification of linkage disequilibrium than other methods under a polygenic model. As small genomic regions are more likely to harbour specific genetic effects, our method is ideal to identify heterogeneity in shared polygenic correlation across regions. We illustrate the usefulness of our method by addressing two questions related to cardio-metabolic traits. First, we explored how regional polygenic correlation can inform on the strong epidemiological association between HDL cholesterol and coronary artery disease (CAD), suggesting a key role for triglycerides metabolism. Second, we investigated the potential role of PPAR{gamma} activators in the prevention of CAD.\n\nConclusionsOur results provide a compelling argument that shared heritability between complex traits is highly heterogeneous across loci.

genetics↗

bioRxiv2017

A machine-learning heuristic to improve gene score prediction of polygenic traitsShort title: Machine-learning boosted gene scores

Machine-learning techniques have helped solve a broad range of prediction problems, yet are not widely used to build polygenic risk scores for the prediction of complex traits. We propose a novel heuristic based on machine-learning techniques (GraBLD) to boost the predictive performance of polygenic risk scores. Gradient boosted regression trees were first used to optimize the weights of SNPs included in the score, followed by a novel regional adjustment for linkage disequilibrium. A calibration set with sample size of ~200 individuals was sufficient for optimal performance. GraBLD yielded prediction R2 of 0.239 and 0.082 using GIANT summary association statistics for height and BMI in the UK Biobank study (N=130K; 1.98M SNPs), explaining 46.9% and 32.7% of the overall polygenic variance, respectively. For diabetes status, the area under the receiver operating characteristic curve was 0.602 in the UK Biobank study using summary-level association statistics from the DIAGRAM consortium. GraBLD outperformed other polygenic score heuristics for the prediction of height (p<2.2x10-16) and BMI (p<1.57x10-4), and was equivalent to LDpred for diabetes. Results were independently validated in the Health and Retirement Study (N=8,292; 688,398 SNPs). Our report demonstrates the use of machine-learning techniques, coupled with summary-level data from large genome-wide meta-analyses to improve the prediction of polygenic traits.

genetics↗