Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

Ho, Daniel Wai‐Hung; Yiu, Wai; Yap, Maurice; Fung, Wai Yan; Ng, Pui Fai; Yip, Shea Ping

doi:10.1371/journal.pone.0026119

Cited by 4 publications

(3 citation statements)

References 22 publications

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“…1). Leptographium longiclavatum and G. clavigera are blue-stain fungal symbiotic species that are believed to play an important role in the mountain pine beetle outbreak in western North America (Lee et al 2006b;DiGuistini et al 2011;Tsui et al 2012 understanding of the population structure and genetic diversity of these fungal species across their range of distribution will provide additional information that can be incorporated into ecological risk modelling of the current outbreak (James et al 2011;De La Giroday et al 2012;Sambaraju et al 2012).…”

Section: Discussionmentioning

confidence: 99%

“…The iPlex Gold assay is a commonly used platform for medium-throughput genotyping, and together with the MassARRAY â System from Sequenom Inc., it has been widely used for fine mapping, validation of genome-wide association studies (GWAS) and routine genetic testing of SNP panels (Ehrich et al 2005;Gabriel et al 2009;Millis 2011). This genotyping platform has been successfully applied to several organisms, including humans, pigs, microorganisms and plants, with reliable results and high proportions of successful SNP validation (Ramos et al 2009;Buggs et al 2010;Bouakaze et al 2011;Ho et al 2011;Shi et al 2011;Syrmis et al 2011).…”

Section: Discussionmentioning

confidence: 99%

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Single‐nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle‐associated symbiotic fungus, using whole‐genome resequencing

Ojeda

Dhillon

Tsui

et al. 2013

Molecular Ecology Resources

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Single-nucleotide polymorphisms (SNPs) are rapidly becoming the standard markers in population genomics studies; however, their use in nonmodel organisms is limited due to the lack of cost-effective approaches to uncover genome-wide variation, and the large number of individuals needed in the screening process to reduce ascertainment bias. To discover SNPs for population genomics studies in the fungal symbionts of the mountain pine beetle (MPB), we developed a road map to discover SNPs and to produce a genotyping platform. We undertook a whole-genome sequencing approach of Leptographium longiclavatum in combination with available genomics resources of another MPB symbiont, Grosmannia clavigera. We sequenced 71 individuals pooled into four groups using the Illumina sequencing technology. We generated between 27 and 30 million reads of 75 bp that resulted in a total of 1, 181 contigs longer than 2 kb and an assembled genome size of 28.9 Mb (N50 = 48 kb, average depth = 125x). A total of 9052 proteins were annotated, and between 9531 and 17,266 SNPs were identified in the four pools. A subset of 206 genes (containing 574 SNPs, 11% false positives) was used to develop a genotyping platform for this species. Using this roadmap, we developed a genotyping assay with a total of 147 SNPs located in 121 genes using the Illumina(®) Sequenom iPLEX Gold. Our preliminary genotyping (success rate = 85%) of 304 individuals from 36 populations supports the utility of this approach for population genomics studies in other MPB fungal symbionts and other fungal nonmodel species.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Single‐nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle‐associated symbiotic fungus, using whole‐genome resequencing

Ojeda

Dhillon

Tsui

et al. 2013

Molecular Ecology Resources

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“…In the initial study, 56 SNPs were grouped together with SNPs of other on-going studies and genotyped by a mass spectrometric method according to the manufacturer’s instructions (Sequenom), as reported previously by our group [ 17 - 19 ]. Sequences of primers for PCR and primer extension (PE) are shown in Additional file 1 .…”

Section: Methodsmentioning

confidence: 99%

Investigating the relationship between UMODL1 gene polymorphisms and high myopia: a case–control study in Chinese

Zhu

Yap

et al. 2012

BMC Med Genet

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BackgroundThe UMODL1 gene was found to be associated with high myopia in Japanese. This study aimed to investigate this gene for association with high myopia in Chinese.MethodsTwo groups of unrelated Han Chinese from Hong Kong were recruited using the same criteria: Sample Set 1 comprising 356 controls (spherical equivalent, SE, within ±1 diopter or D) and 356 cases (SE ≤ −8D), and Sample Set 2 comprising 394 controls and 526 cases. Fifty-nine tag single nucleotide polymorphisms (SNPs) were selected and genotyped for Sample Set 1. Four SNPs were followed up with Sample Set 2. Both single-marker and haplotype analyses were performed with cases defined by different SE thresholds. Secondary phenotypes were also analyzed for association with genotypes.ResultsData filtering left 57 SNPs for analysis. Single-marker analysis did not reveal any significant differences between cases and controls in the initial study. However, haplotype GCT for markers rs220168-rs220170-rs11911271 showed marginal significance (empirical P = 0.076; SE ≤ −12D for cases), but could not be replicated in the follow-up study. In contrast, non-synonymous SNP rs3819142 was associated with high myopia (SE ≤ −10D) in the follow-up study, but could not be confirmed using Sample Set 1. The SNP rs2839471, positive in the original Japanese study, gave negative results in all our analyses. Exploratory analysis of secondary phenotypes indicated that allele C of rs220120 was associated with anterior chamber depth (adjusted P = 0.0460).ConclusionsCommon UMODL1 polymorphisms were unlikely to be important in the genetic susceptibility to high myopia in Han Chinese.

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Genetic variants in the transcription regulatory region of MEGF10 are associated with autism in Chinese Han population

Qin

You

et al. 2017

Sci Rep

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Multiple epidermal growth factor-like-domains 10 (MEGF10), a critical member of the apoptotic engulfment pathway, mediates axon pruning and synapse elimination during brain development. Previous studies indicated that synaptic pruning deficit was associated with autism-related phenotypes. However, the relationship between MEGF10 and autism remains poorly understood. Disease-associated variants are significantly enriched in the transcription regulatory regions. These include the transcription start site (TSS) and its cis-regulatory elements. To investigate the role of MEGF10 variants with putative transcription regulatory function in the etiology of autism, we performed a family-based association study in 410 Chinese Han trios. Our results indicate that three single nucleotide polymorphisms (SNPs), rs4836316, rs2194079 and rs4836317 near the TSS are significantly associated with autism following Bonferroni correction (p = 0.0011, p = 0.0088, and p = 0.0023, respectively). Haplotype T-A-G (rs4836316-rs2194079-rs4836317) was preferentially transmitted from parents to affected offspring (p permutation = 0.0055). Consistently, functional exploration further verified that the risk allele and haplotype might influence its binding with transcription factors, resulting in decreased transcriptional activity of MEGF10. Our findings indicated that the risk alleles and haplotype near the MEGF10 TSS might modulate transcriptional activity and increase the susceptibility to autism.

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Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

Cited by 4 publications

References 22 publications

Single‐nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle‐associated symbiotic fungus, using whole‐genome resequencing

Single‐nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle‐associated symbiotic fungus, using whole‐genome resequencing

Investigating the relationship between UMODL1 gene polymorphisms and high myopia: a case–control study in Chinese

Genetic variants in the transcription regulatory region of MEGF10 are associated with autism in Chinese Han population

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