Biology subjects

Murphy, R.

Publications and source records attributed to Murphy, R..

2 recordsLinked to original sources

bioRxiv2017

Discordant association of the CREBRF rs373863828 minor allele with increased body mass index and protection from type 2 diabetes in Maori and Pacific (Polynesian) people living in New Zealand

Aim/HypothesesThe minor allele of CREBRF rs373863828 associates with increased body mass index (BMI) and reduced risk of type 2 diabetes (T2D) in the Samoan population of Samoa and American Samoa. Our aim was to test rs373863828 for association with BMI and odds of T2D, gout and chronic kidney disease (CKD) in M[a]ori and Pacific (Polynesian) people living in Aotearoa New Zealand in 2,286 adults.\n\nMethodsAssociation analyses were performed by linear and logistic regression with BMI, log-transformed BMI, waist circumference, T2D, gout and CKD. Analyses were adjusted for age, sex, the first four genome-wide principal components, and (when appropriate) BMI, waist circumference and T2D.\n\nResultsFor the minor allele of rs373863828 the effect size for log-transformed BMI was 0.038 (95% CI [0.022-0.055], P=4.8x10-6) and for T2D was OR=0.59 (95% CI [0.47-0.73], P=1.9x10-6). There was no evidence for association of genotype with variance in BMI (P=0.13). Nor was there evidence for association with serum urate ({beta}=0.012 mmol/L, Pc=0.10), gout (OR=1.00, P=0.98) or CKD (OR=0.91, P=0.59).\n\nConclusions/interpretationOur results replicated, with very similar effect sizes, association of the minor allele of rs373863828 with higher BMI but lower odds of T2D among New Zealand Polynesian adults, as in Samoan adults living in Samoa and American Samoa.

genetics↗

bioRxiv2016

An improved de novo pipeline for enrichment of high diversity mitochondrial genomes from Amphibia to high-throughput sequencing

We present an improved de novo pipeline by combining long-range polymerase chain reaction (LR-PCR) and capture hybridization for enriching mitochondrial DNA to high-throughput sequencing. We test a new set of primers and hybridizing long-range library (LR-HY) with 112 mitochondrial genomes (MtG) representing three orders, 12 families, 54 genera, and 106 species of Amphibia. The primers are used for obtaining wide taxonomic MtG amplicons to sequence directly and/or make probes for closely related species. LR-HY is compared to standard hybridization. The primers successfully amplify 82 MtGs from all three order, all families, 92.6% (50/54) of the genera, and 74.5% (79/106) of the species, despite some DNA degradation and gene rearrangement. We observe a significantly negative correlation between sequence depth and gene variation. The pattern of highly variable regions is separately distributed in different regions within the length of < 4 kb in the 33-pooled sample. We demonstrate that using 2 kb libraries generate deeper sequence coverage in the highly variable loci than using 400 bp libraries. In total, the pipeline successfully recovers 83 complete and 14 almost complete MtGs from 53 of 54 genera, including 14 MtGs had rearranged protein-coding genes. This universal primers combined with LR-HY is an efficient way to enrich complete MtGs across the entire Amphibia.

genomics↗