Identification and characterization of novel rapidly mutating Y-chromosomal short tandem repeat markers.

Short tandem repeat polymorphisms on the male-specific part of the human Y-chromosome (Y-STRs) are valuable tools in many areas of human genetics. Although their paternal inheritance and moderate mutation rate (~10 mutations per marker per meiosis) allow detecting paternal relationships, they typically fail to separate male relatives. Previously, we identified 13 Y-STR markers with untypically high mutation rates (>10 ), termed rapidly mutating (RM) Y-STRs, and showed that they improved male relative differentiation over standard Y-STRs.

Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers.

A Japanese-specific allele in the GALNT11 gene.

In this study, five single nucleotide polymorphisms (SNPs) in the ABCC4, FBN1, CEP152, ZNF804B, and GALNT11 genes were investigated to assess allele frequencies in 14 different populations by a novel pentaplex PCR method. All SNPs were polymorphic in East Asians, whereas mutant alleles were absent or rare in non-East Asians. The frequencies of a mutant allele in FBN1 (rs140598) showed a north-south downward cline in East Asia, whereas those of a mutant allele in ZNF804B (rs1916830) were relatively uniform in East Asia.

A hypervariable STR polymorphism in the complement factor I (CFI) gene: Asian-specific alleles.

In this study, a short tandem repeat (STR) polymorphism in intron 7 of the human complement factor I (CFI) gene was studied in 637 DNA samples obtained from African, German, Thai, and Japanese populations and German and Japanese families. A total of 41 alleles were observed and classified into two groups, L and H, based on size differences. Group H, which consisted of 16 alleles, was observed only in Thai and Japanese populations at frequencies of 0.

HERC1 polymorphisms: population-specific variations in haplotype composition.

Human HERC1 is one of six HERC proteins and may play an important role in intracellular membrane trafficking. The human HERC1 gene is suggested to have been affected by local positive selection. To assess the global frequency distributions of coding and non-coding single nucleotide polymorphisms (SNPs) in the HERC1 gene, we developed a new simultaneous genotyping method for four SNPs, and applied this method to investigate 1213 individuals from 12 global populations.

Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTR Yfiler PCR amplification kit.

The Y-chromosomal short tandem repeat (Y-STR) polymorphisms included in the AmpFlSTR Yfiler polymerase chain reaction amplification kit have become widely used for forensic and evolutionary applications where a reliable knowledge on mutation properties is necessary for correct data interpretation. Therefore, we investigated the 17 Yfiler Y-STRs in 1,730-1,764 DNA-confirmed father-son pairs per locus and found 84 sequence-confirmed mutations among the 29,792 meiotic transfers covered. Of the 84 mutations, 83 (98.

A paternity case with three genetic incompatibilities between father and child due to maternal uniparental disomy 21 and a mutation at the Y chromosome.

A parentage case is described that revealed a potentially erroneous exclusion from paternity in three systems, two on chromosome 21 and one on chromosome Y. Follow-up tests, especially of chromosome 21, were subsequently performed. Actually, the child's chromosome 21 showed alleles of maternal but not of paternal origin being consistent with a maternal uniparental disomy of chromosome 21.

Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations.

The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed among 2176 unrelated individuals from 6 regional Polish populations and among 4321 individuals from Germany (three samples), Austria, The Netherlands, Sweden, Czech Republic, Slovakia, Belarus, Ukraine and the Russian Federation (six samples). The statistical approach consisted of AMOVA, calculation of pairwise Rst values and analysis by multidimensional scaling.

New alleles and mutational events at 14 STR loci from different German populations.

The molecular origin of DNA mutations and the mutation rates were analyzed at 14 short tandem repeat (STR) loci with samples from trio cases derived from 10 different German population samples. STR loci comprised of D2S1360, D3S1744, D4S2366, D5S2500, D6S474, D7S1517, D8S1132, D10S2325, D12S391, D18S51, D19S246, D20S480, D21S226, and D22S689. In a total of 488 meioses, 16 isolated genetic inconsistencies in 8 different STRs were observed, whereas no mutations were found at the other loci.

Molecular basis of complement factor I (CFI) polymorphism: one of two polymorphic suballeles responsible for CFI A is Japanese-specific.

Isoelectric focusing has revealed that human complement factor I (CFI) is controlled by two polymorphic alleles, CFI(*)A and CFI(*)B, and a few rare variant alleles. In this study the molecular basis of the CFI polymorphism was investigated in 174 Japanese. The CFI(*)A was divided into two suballeles, CFI(*)As (R201S) and CFI(*)Ah (R406H).

Validation of a "new" short tandem repeat (STR) fluorescent multiplex system and report of population genetic data.

The Humantype Chimera PCR Amplification Kit contains 12 polymorphic loci (ACTBP2 (= SE33), D18S51, D4S2366, D6S474, D8S1132, D12S391, D2S1360, D3S1744, D5S2500, D7S1517, D10S2325, D21S2055), of which the latter 10 loci have not been used extensively for human identity testing. The sex determinant locus amelogenin is also included in the kit. Amplification was successful on a variety of thermal cyclers and the amplicons could be analyzed on both the ABI PRISM 310 and 3100 Genetic Analyzers.

OCA2 481Thr, a hypofunctional allele in pigmentation, is characteristic of northeastern Asian populations.

Asians as well as Europeans have light skin, for which no genes to date are known to be responsible. A mutation, Ala481Thr (c.G1559A), in the oculocutaneous albinism type II (OCA2) gene has approximately 70% function of the wild type allele in melanogenesis.

Detection of manipulation in doping control urine sample collection: a multidisciplinary approach to determine identical urine samples.

Manipulation of urine sampling in sports drug testing is considered a violation of anti-doping rules and is consequently sanctioned by regulatory authorities. In 2003, three identical urine specimens were provided by three different athletes, and the identity of all urine samples was detected and substantiated using numerous analytical strategies including gas chromatography-mass spectrometry with steroid and metabolite profiling, gas chromatography-nitrogen/phosphorus detector analysis, high-performance liquid chromatography-UV fingerprinting, and DNA-STR (short tandem repeat) analysis. None of the respective athletes was the donor of the urine provided for doping analysis, which proved to be a urine sample collected from other unidentified individual(s).

Searching for the origin of Romanies: Slovakian Romani, Jats of Haryana and Jat Sikhs Y-STR data in comparison with different Romani populations.

Haplotype frequencies for 11 Y-STR markers (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) in a Romani population (n=63) from Slovakia, Jats of Haryana (n=84) and Jat Sikhs (n=80) from India were determined. The Slovakian Romani, the Haryana and Sikh populations were endogamous based on their unique haplotype ratio and haplotype diversity values, although the Sikh population appeared to be more diverse. AMOVA revealed non-significant differences between the Romanies and significant differences with non-Romani populations.

The structure and diversity of alpha1-acid glycoprotein/orosomucoid gene in Africans.

Human orosomucoid (ORM), or alpha(1)-acid glycoprotein, is known to be controlled by duplicated and triplicated genes on chromosome 9, encoding ORM1 and ORM2 proteins. In this study, the structure and diversity of the ORM gene were investigated in 16 Sub-Saharan Africans, who originated from widely dispersed locations in Africa. The duplicated ORM1-ORM2 gene was observed in all 16 samples.

Which short tandem repeat polymorphisms are required for identification? Lessons from complicated kinship cases.

This paper presents 5 examples of complicated deficient parentage cases, which were sufficiently resolved by extensive DNA typing using short tandem repeat (STR) and restriction fragment length polymorphisms (RFLPs). The latter have greatly contributed to the solution of deficiency cases, although their application is only feasible, if high molecular weight DNA and time are in abundance. This apart, RFLP technique is available in a few laboratories only, and its extinction can be expected in medium term.

Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis.

To test for human population substructure and to investigate human population history we have analysed Y-chromosome diversity using seven microsatellites (Y-STRs) and ten binary markers (Y-SNPs) in samples from eight regionally distributed populations from Poland (n = 913) and 11 from Germany (n = 1,215). Based on data from both Y-chromosome marker systems, which we found to be highly correlated (r = 0.96), and using spatial analysis of the molecular variance (SAMOVA), we revealed statistically significant support for two groups of populations: (1) all Polish populations and (2) all German populations.

Molecular basis of ESD*5 and ESD*7 and haplotype analysis with new polymorphisms in introns.

The two polymorphic alleles of esterase D (ESD), ESD*5 and ESD*7, are specific to Europeans and Asians, respectively. In this study the molecular basis was characterized: ESD*5, arising from ESD*1, has a G to A transition, resulting in Gly257(GGT) --> Asp(GAT); and ESD*7, originating from ESD*2, has an A to G transition, resulting in Asp231(GAT) --> Gly(GGT). Glycine is also involved in the common ESD*1/ESD*2 polymorphism [Gly190(GGA) --> Glu(GAA)].

Penetrating limbo-keratoplasty for granular and lattice corneal dystrophy: survival of donor limbal stem cells and intermediate-term clinical results.

Purpose: To assess clinical follow-up data, and to identify donor epithelial cells after homologous penetrating central limbo-keratoplasty in patients with granular and lattice corneal dystrophies compared with patients who underwent conventional penetrating keratoplasty (PK).

Design: Mixed retrospective and prospective nonrandomized comparative case series.

Participants And Controls: Twenty-six patients who underwent 33 limbo-keratoplasty procedures for granular or lattice corneal dystrophy since May 1995 and a historical control group of 24 patients who underwent 36 PK procedures between November 1986 and May 1995.

Long-term results of allogeneic penetrating limbo-keratoplasty in total limbal stem cell deficiency.

Objective: To determine the prognosis of allogeneic penetrating limbo-keratoplasty in patients with total limbal stem cell deficiency and to find out if donor limbal stem cells survive in the long run.

Design: Noncomparative prospective case series.

Participants: Forty-eight patients with total limbal stem cell deficiency.

Asian online Y-STR Haplotype Reference Database.

For several years Y-chromosomal microsatellites (short tandem repeats, STRs) have been well established in forensic practice. In this context, the genetic characteristics of the Y chromosome (i.e.

A comprehensive analysis of recently integrated human Ta L1 elements.

The Ta (transcribed, subset a) subfamily of L1 LINEs (long interspersed elements) is characterized by a 3-bp ACA sequence in the 3' untranslated region and contains approximately 520 members in the human genome. Here, we have extracted 468 Ta L1Hs (L1 human specific) elements from the draft human genomic sequence and screened individual elements using polymerase-chain-reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity. One hundred twenty-four of the elements amenable to complete sequence analysis were full length ( approximately 6 kb) and have apparently escaped any 5' truncation.