7 research outputs found
Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe
Analysis of 8 X-chromosomal markers in the population of central Croatia
Aim To analyze 8 X-linked short tandem repeat (STR) markers
in the population of central Croatia and to evaluate
their forensic efficiency.
Methods We carried out a statistical analysis of the data
from previously performed genetic analyses, collected
during routine forensic work by the Forensic Science Centre
‘‘Ivan Vučetić.’’ Mentype® Argus X-8 PCR amplification kit
was used for typing the data of 99 unrelated healthy women
and 78 men from central Croatia. Haplotype frequencies
were calculated only in male samples. Arlequin 3.5
software was used to assess Hardy-Weinberg equilibrium
(HWE), linkage disequilibrium (LD), observed and expected
heterozygosity. Power of discrimination (PD) for men and
women, polymorphism information content (PIC), power
of exclusion, and mean exclusion chance for deficiency
cases, normal trios, and duos were determined using online
database ChrX-STR.org.
Results In female samples, deviations from HWE (P = 0.006)
for each locus were not found. LD test performed both
on female and male samples revealed no significant association
between markers (P = 0.002). DXS10135 was
the most polymorphic locus (PIC = 0.931). PD varied from
0.692 to 0.935 in male and from 0.845 to 0.992 in female
samples. Combined PD reached 99.999999% in men and
99.9999999999% in women.
Conclusion Performed analyses revealed that the studied
marker set contained polymorphic markers with high
power of discrimination. We can conclude that Mentype®
Argus X-8 PCR is suitable for application in the population
of central Croatia. Results of this study, together with collected
allele and haplotype frequencies, are the first step
in establishing a national reference X-STR database based
on 8 X-STR loci
Analysis of 8 X-chromosomal markers in the population of central Croatia FORENSIC SCIENCE
Aim To analyze 8 X-linked short tandem repeat (STR) markers in the population of central Croatia and to evaluate their forensic efficiency. Methods We carried out a statistical analysis of the data from previously performed genetic analyses, collected during routine forensic work by the Forensic Science Centre ''Ivan Vučetić. '' Mentype® Argus X-8 PCR amplification kit was used for typing the data of 99 unrelated healthy women and 78 men from central Croatia. Haplotype frequencies were calculated only in male samples. Arlequin 3.5 software was used to assess Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), observed and expected heterozygosity. Power of discrimination (PD) for men and women, polymorphism information content (PIC), power of exclusion, and mean exclusion chance for deficiency cases, normal trios, and duos were determined using online database ChrX-STR.org. Results In female samples, deviations from HWE (P = 0.006) for each locus were not found. LD test performed both on female and male samples revealed no significant association between markers (P = 0.002). DXS10135 was the most polymorphic locus (PIC = 0.931). PD varied from 0.692 to 0.935 in male and from 0.845 to 0.992 in female samples. Combined PD reached 99.999999% in men and 99.9999999999% in women. Conclusion Performed analyses revealed that the studied marker set contained polymorphic markers with high power of discrimination. We can conclude that Mentype ® Argus X-8 PCR is suitable for application in the population of central Croatia. Results of this study, together with collected allele and haplotype frequencies, are the first step in establishing a national reference X-STR database based on 8 X-STR loci
A global analysis of Y-chromosomal haplotype diversity for 23 STR loci
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.Peer reviewe
Analysis of 8 X-chromosomal markers in the population of central Croatia
Aim To analyze 8 X-linked short tandem repeat (STR) markers
in the population of central Croatia and to evaluate
their forensic efficiency.
Methods We carried out a statistical analysis of the data
from previously performed genetic analyses, collected
during routine forensic work by the Forensic Science Centre
‘‘Ivan Vučetić.’’ Mentype® Argus X-8 PCR amplification kit
was used for typing the data of 99 unrelated healthy women
and 78 men from central Croatia. Haplotype frequencies
were calculated only in male samples. Arlequin 3.5
software was used to assess Hardy-Weinberg equilibrium
(HWE), linkage disequilibrium (LD), observed and expected
heterozygosity. Power of discrimination (PD) for men and
women, polymorphism information content (PIC), power
of exclusion, and mean exclusion chance for deficiency
cases, normal trios, and duos were determined using online
database ChrX-STR.org.
Results In female samples, deviations from HWE (P = 0.006)
for each locus were not found. LD test performed both
on female and male samples revealed no significant association
between markers (P = 0.002). DXS10135 was
the most polymorphic locus (PIC = 0.931). PD varied from
0.692 to 0.935 in male and from 0.845 to 0.992 in female
samples. Combined PD reached 99.999999% in men and
99.9999999999% in women.
Conclusion Performed analyses revealed that the studied
marker set contained polymorphic markers with high
power of discrimination. We can conclude that Mentype®
Argus X-8 PCR is suitable for application in the population
of central Croatia. Results of this study, together with collected
allele and haplotype frequencies, are the first step
in establishing a national reference X-STR database based
on 8 X-STR loci
Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysi
Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
Relevant for various areas of human genetics,
Y-chromosomal short tandem repeats (Y-STRs) are com-
monly used for testing close paternal relationships among
individuals and populations, and for male lineage iden-
tification. However, even the widely used 17-loci Yfiler
set cannot resolve individuals and populations completely.
Here, 52 centers generated quality-controlled data of 13
rapidly mutating (RM) Y-STRs in 14,644 related and
unrelated males from 111 worldwide populations. Strik-
ingly, >99% of the 12,272 unrelated males were com-
pletely individualized. Haplotype diversity was extremely
high (global: 0.9999985, regional: 0.99836\u20130.9999988).
Haplotype sharing between populations was almost ab-
sent except for six (0.05%) of the 12,156 haplotypes.
Haplotype sharing within populations was generally rare
(0.8% nonunique haplotypes), significantly lower in ur-
ban (0.9%) than rural (2.1%) and highest in endogamous
groups (14.3%). Analysis of molecular variance revealed
99.98% of variation within populations, 0.018% among
populations within groups, and 0.002% among groups. Of
the 2,372 newly and 156 previously typed male relative
pairs,29% were differentiated including 27% of the 2,378
father\u2013son pairs. Relative to Yfiler, haplotype diversity
was increased in 86% of the populations tested and over-
all male relative differentiation was raised by 23.5%. Our
study demonstrates the value of RM Y-STRs in identifying
and separating unrelated and related males and provides a
reference database