Analysis of 17 STR data on 5362 southern Portuguese individuals—an update on reference database

Silva, Raquel Cabezas; Ribeiro, Teresa; Lucas, I.; Porto, Maria João; Santos, Jorge Costa; Dario, Paulo

doi:10.1016/j.fsigen.2015.11.007

Cited by 21 publications

(6 citation statements)

References 18 publications

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“…Genetic variations in this region can cause various pathophysiological alterations. 24 This site may therefore be a target region of transcription factors and cis -regulatory elements that can influence EFHD2 expression by regulating the expression and stability of mRNA. EFHD2 is a Ca 2+ -binding protein that regulates Ca 2+ ion concentrations.…”

Section: Discussionmentioning

confidence: 99%

“…EFHD2 is a Ca 2+ -binding protein that regulates Ca 2+ ion concentrations. 24 The actions of Ca 2+ are considered pivotal in the dopamine hypothesis of SCZ, 17 thus suggesting the involvement of EFHD2 in SCZ.…”

Section: Discussionmentioning

confidence: 99%

“…PowerStats 1.2 software (Promega, Madison, WI, USA) 24 was used to calculate the genotype and allele frequencies, as well as the frequencies of the dominant, recessive, codominant, and superdominant models. The Hardy–Weinberg equilibrium test and linkage disequilibrium analysis were performed using Haploview 4.0 software (Broad Institute, Cambridge, MA, USA).…”

Section: Methodsmentioning

confidence: 99%

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Association betweenEFHD2gene polymorphisms and schizophrenia among the Han population in northern China

Gao

Zeng

et al. 2020

J Int Med Res

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Objective Schizophrenia is a severe neurodevelopmental disorder with a complex genetic and environmental etiology. The gene encoding EF-hand domain-containing protein D2 ( EFHD2) may be a genetic risk locus for schizophrenia. Methods We genotyped four EFHD2 single-nucleotide polymorphisms (281 schizophrenia cases [SCZ], 321 controls) from northern Chinese Han individuals using Sanger sequencing and polymerase chain reaction-restriction fragment length polymorphism analysis. Differences existed in genotype, allele, and haplotype frequency distributions between SCZ and control groups. Results The rs2473357 genotype and allele frequency distributions differed between SCZ and controls; however, this difference disappeared after Bonferroni correction. Differences in rs2473357 genotype and allele frequency distributions between SCZ and controls were more pronounced in men than in women. The G allele increased schizophrenia risk (odds ratio = 1.807, 95% confidence interval = 1.164–2.803). Among six haplotypes (G–, A–, G-insC, A-C, G-C, and G-T), the G– haplotype frequency distribution differed between SCZ and controls in women; the A-C and G-C haplotype frequency distributions differed between SCZ and controls in men. Conclusions EFHD2 may be involved in schizophrenia. Sex differences in EFHD2 genotype and allele frequency distributions existed among schizophrenia patients. Further research is needed to determine the role of EFHD2 in schizophrenia.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Association betweenEFHD2gene polymorphisms and schizophrenia among the Han population in northern China

Gao

Zeng

et al. 2020

J Int Med Res

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“…The values for matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), power of exclusion (PE), typical paternity index, gene diversity (GD), and heterozygosity (He) were calculated using PowerStats v1.2 software (Tereba, ), which was modified by Cabezas Silva et al. to support and manage a large number of samples (Cabezas Silva et al., ). Reynolds’ genetic distance based on allele frequencies across the 15 autosomal loci shared by the compared populations and exact test P ‐values were generated using PowerMarker V3.25.…”

Section: Methodsmentioning

confidence: 99%

Genetic polymorphisms, forensic efficiency, and phylogenetic analysis of 15 autosomal STR loci in the Uygur population of Ili Kazakh Autonomous Prefecture, Northwestern China

Feng

Wang

Hyeong-keun

et al. 2018

Annals of Human Genetics

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The genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analyzed in 449 individuals of the Uygur population from Ili Kazakh Autonomous Prefecture, Northwestern China. Phylogenetic analysis was performed among the Ili Uygur population and other relevant populations. The neighbor-joining tree and multidimensional scaling plot were generated based on the Nei's standard genetic distance. We found a total of 173 alleles with corresponding frequencies ranging from 0.5022 to 0.0011. The combined powers of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999985 and 0.99999880065, respectively. Population comparisons indicated that the Ili Uygur population had a relatively close genetic relationship with the Uygur populations from other regions of China. The pairwise genetic distance and P-values between Ili Uygur and 10 published populations showed that no statistically significant differences existed between the Ili Uygur population and the Kashi, Kashgar, and Kotan Uygur. Therefore, the Ili Uygur population has its own unique Uygur genetic characteristics that were different from the other ethnic populations of China.

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“…For autosomal loci, sample allele frequencies and exact Hardy-Weinberg equilibrium (HWE) tests were calculated using PowerMarker v3.25 [ 14 ]. Values for power of discrimination (DP), polymorphism information content (PIC), power of exclusion (PE), and heterozygosity (He) were calculated using Power Stats v1.2 software [ 17 ] that had been modified by Raquel, et al to support and manage the large amount of samples [ 18 ]. Pairwise genetic distance ( Fst ) and p values for each locus were calculated between populations using Arlequin v3.5 software [ 15 ].…”

Section: Methodsmentioning

confidence: 99%

Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China

Yao

Wang

2016

PLoS ONE

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In the present study, we investigated the genetic characteristics of 25 Y-chromosomal and 15 autosomal short tandem repeat (STR) loci in 305 unrelated Han Chinese male individuals from Liaoning Province using AmpFISTR® Yfiler® Plus and IdentifilerTM PCR amplification kits. Population comparison was performed between Liaoning Han population and different ethnic groups to better understand the genetic background of the Liaoning Han population. For Y-STR loci, the overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. Gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Rst and two multi-dimensional scaling plots showed that minor differences were observed when the Liaoning Han population was compared to the Jilin Han Chinese, Beijing Han Chinese, Liaoning Manchu, Liaoning Mongolian, Liaoning Xibe, Shandong Han Chinese, Jiangsu Han Chinese, Anhui Han Chinese, Guizhou Han Chinese and Liaoning Hui populations; by contrast, major differences were observed when the Shanxi Han Chinese, Yunnan Bai, Jiangxi Han Chinese, Guangdong Han Chinese, Liaoning Korean, Hunan Tujia, Guangxi Zhuang, Gansu Tibetan, Xishuangbanna Dai, South Korean, Japanese and Hunan Miao populations. For autosomal STR loci, DP ranged from 0.9621 (D2S1338) to 0.8177 (TPOX), with PE distributing from 0.7521 (D18S51) to 0.2988 (TH01). A population comparison was performed and no statistically significant differences were detected at any STR loci between Liaoning Han, China Dong, and Shaanxi Han populations. The results showed that the 25 Y-STR and 15 autosomal STR loci in the Liaoning Han population were valuable for forensic applications and human genetics, and Liaoning Han was an independent endogenous ethnicity with a unique subpopulation structure.

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Analysis of 17 STR data on 5362 southern Portuguese individuals—an update on reference database

Cited by 21 publications

References 18 publications

Association betweenEFHD2gene polymorphisms and schizophrenia among the Han population in northern China

Association betweenEFHD2gene polymorphisms and schizophrenia among the Han population in northern China

Genetic polymorphisms, forensic efficiency, and phylogenetic analysis of 15 autosomal STR loci in the Uygur population of Ili Kazakh Autonomous Prefecture, Northwestern China

Genetic Variation of 25 Y-Chromosomal and 15 Autosomal STR Loci in the Han Chinese Population of Liaoning Province, Northeast China

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