Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs

Pakstis, Andrew J.; Gürkan, Cemal; Doğan, Mustafa; Balkaya, Hasan Emin; Doğan, Serkan; Neophytou, Pavlos; Cherni, Lotfi; Boussetta, Sami; Khodjet‐El‐Khil, Houssein; Elgaaied, Amel Ben Ammar; Salvo, Nina Mjølsnes; Janssen, Kirstin; Olsen, Gunn-Hege; Hadi, Sibte; Almohammed, Eida Khalaf; Pereira, Vânia; Truelsen, Ditte; Bülbül, Özlem; Soundararajan, Usha; Rajeevan, Haseena; Kidd, Judith R.; Kídd, Kenneth K.

doi:10.1038/s41431-019-0466-6

Cited by 26 publications

(29 citation statements)

References 23 publications

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“…29 The Northern European and Mediterranean European populations, which comprise the majority of the Australian ALS cohort, exhibit distinct genotype clusters when compared to Japanese and Korean populations. 30 Consequently, it could also be argued that subtle genetic differences could affect the pathogenic processes underlying ALS development across different ethnic groups, with Japanese and South Korean patients being more resistant to developing ALS. While subtle differences in slope estimates were evident, with 5 steps modeled for the South Korean patients, the strong linear relationship between log age and log incidence across the 3 populations suggests that ALS is a multistep process irrespective of ethnic origins.…”

Section: Pathophysiologic Mechanisms Underlying Alsmentioning

confidence: 99%

ALS is a multistep process in South Korean, Japanese, and Australian patients

Vucic¹,

Higashihara²,

Sobue³

et al. 2020

Neurology

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ObjectiveTo establish whether amyotrophic lateral sclerosis (ALS) is a multistep process in South Korean and Japanese populations when compared to Australian cohorts.MethodsWe generated incident data by age and sex for Japanese (collected between April 2009 and March 2010) and South Korean patients with ALS (collected between January 2011 and December 2015). Mortality rates were provided for Australian patients with ALS (collected between 2007 and 2016). We regressed the log of age-specific incidence against the log of age with least squares regression for each ALS population.ResultsWe identified 11,834 cases of ALS from the 3 populations, including 6,524 Australian, 2,264 Japanese, and 3,049 South Korean ALS cases. We established a linear relation between the log incidence and log age in the 3 populations: Australia r2 = 0.99, Japan r2 = 0.99, South Korea r2 = 0.99. The estimate slopes were similar across the 3 populations, being 5.4 (95% confidence interval [CI], 4.8–5.5) in Japanese, 5.4 (95% CI, 5.2–5.7) in Australian, and 4.4 (95% CI, 4.2–4.8) in South Korean patients.ConclusionsThe linear relationship between log age and log incidence is consistent with a multistage model of disease, with slope estimated suggesting that 6 steps were required in Japanese and Australian patients with ALS while 5 steps were needed in South Korean patients. Identification of these steps could identify novel therapeutic strategies.

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Section: Pathophysiologic Mechanisms Underlying Alsmentioning

confidence: 99%

ALS is a multistep process in South Korean, Japanese, and Australian patients

Vucic¹,

Higashihara²,

Sobue³

et al. 2020

Neurology

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“…Were it not for the large number of MH in the analysis, this would be a trivial difference but it is likely to be meaningful when examined in the context of larger European and SW Asian populations [34]. We chose to sequence individuals from diverse populations in the initial analysis and later focused on the three East African populations and one Southeastern European population.…”

Section: Discussionmentioning

confidence: 99%

Validation of novel forensic DNA markers using multiplex microhaplotype sequencing

Gandotra¹,

Speed²,

Qin

et al. 2020

Forensic Science International: Genetics

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Microhaplotypes (MH) are comprised of multiple single nucleotide polymorphisms (SNPs) that are located within 300 bases of genomic sequence. Improved tools are needed to facilitate broader application of microhaplotypes in a diverse range of populations and forensic settings. We designed an assay for multiplex sequencing of 90 microhaplotypes (mMHseq) that include 46 MH loci with high Effective Number of Alleles (A e) from previous studies [1], and 44 high A e MH loci containing between four to fourteen SNPs that were identified from the 1000 Genomes (1KG) Project. The unique design of mMHseq integrates a novel method for multiplex amplification from small DNA amounts, and multiplex sequencing of 48 samples in a single MiSeq run to detect all relevant MH variation. Assay performance was evaluated in a cohort of 156 individuals from seven different world populations from Africa, Asia, and Europe. Three of those populations from East Africa (Chagga, Sandawe, and Zaramo) and one from Eastern Europe (Adygei) had sufficient individuals sequenced by the assay to be included in statistical analyses with the 26 1KG populations. For those 30 populations the mean global average A e was 5.08 (range: 2.7-11.54) and mean informativeness for biogeographic variation (I n) was 0.30 (range: 0.08-0.70). Eighty-five novel SNPs were detected in 58 of the 90 microhaplotypes. Open-source, web-based software was developed to visualize haplotype phase data for each microhaplotype and individual. Our approach for multiplex microhaplotype sequencing can be customized and expanded as novel loci are being discovered.

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“…This can be explained by STRU CTU RE handling autosomal markers differently from the haploid markers, since in autosomal analysis STRU CTU RE will define clusters by finding Mendelian populations of individuals. Another factor could be the number of individuals in each input population, with more in the Y-STR than the SNPs analysis 27 . Increasing the number of the Kidd Ancestry Informative SNP markers might improve its HapMap discriminatory power between the overlapping populations.…”

Section: Discussionmentioning

confidence: 99%

“…Population structure was investigated using the program STRU CTU RE version 2.3.7 50 with an admixture model. The HapMap was generated for two panels, the 55 Kidd Ancestry Informative SNPs (AISNPs) genotypes of 140 populations (8,148 individuals) 27 and Y-STR data for 19 markers of 134 populations (21,323 individuals) [14][15][16][17] . Four markers were excluded from the PowerPlex Y23 System, the two rapidly mutating STR (DYS570, DYS576), and the markers (DYS549, DYS643), so that more Middle Eastern populations could be included in this analysis.…”

Section: Discussionmentioning

confidence: 99%

Population genetic diversity in an Iraqi population and gene flow across the Arabian Peninsula

Lazim

Almohammed

Hadi

et al. 2020

Sci Rep

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Y-STRs have emerged as important forensic and population genetic markers for human identification and population differentiation studies. Therefore, population databases for these markers have been developed for almost all major populations around the world. The Iraqi population encompasses several ethnic groups that need to be genetically characterised and evaluated for possible substructures. Previous studies on the Iraqi population based on Y-STR markers were limited by a restricted number of markers. A larger database for Iraqi Arab population needed to be developed to help study and compare the population with other Middle Eastern populations. Twenty-three Y-STR loci included in the PowerPlex Y23 (Promega, Madison, WI, USA) were typed in 254 males from the Iraqi Arab population. Global and regional Y-STR analysis demonstrated regional genetic continuity among the populations of Iraq, the Arabian Peninsula and the Middle East. The Iraqi Arab haplotypes were used to allocate samples to their most likely haplogroups using Athey’s Haplogroup Predictor tool. Prediction indicated predominance (36.6%) of haplogroup J1 in Iraqi Arabs. The migration rate between other populations and the Iraqis was inferred using coalescence theory in the Migrate-n program. Y-STR data were used to test different out-of-Africa migration models as well as more recent migrations within the Arabian Peninsula. The migration models demonstrated that gene flow to Iraq began from East Africa, with the Levantine corridor the most probable passageway out of Africa. The data presented here will enrich our understanding of genetic diversity in the region and introduce a PowerPlex Y23 database to the forensic community.

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Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs

Cited by 26 publications

References 23 publications

ALS is a multistep process in South Korean, Japanese, and Australian patients

ALS is a multistep process in South Korean, Japanese, and Australian patients

Validation of novel forensic DNA markers using multiplex microhaplotype sequencing

Population genetic diversity in an Iraqi population and gene flow across the Arabian Peninsula

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