Evaluation of Y-chromosomal STRs: a multicenter study

A multicenter study has been carried out to characterize 13 polymorphic short tandem repeat (STR) systems located on the male specific part of the human Y chromosome (DYS19, DYS288, DYS385, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, YCAI, YCAII, YCAIII, DXYS156Y). Amplification parameters and electrophoresis protocols including multiplex approaches were compiled. The typing of non-recombining Y loci with uniparental inheritance requires special attention to population substructuring due to prevalent male lineages. To assess the extent of these subheterogeneities up to 3825 unrelated males were typed in up to 48 population samples for the respective loci. A consistent repeat based nomenclature for most of the loci has been introduced. Moreover we have estimated the average mutation rate for DYS19 in 626 confirmed father-son pairs as 3.2 × 10^–3 (95% confidence interval limits of 0.00041–0.00677), a value which can also be expected for other Y-STR loci with similar repeat structure. Recommendations are given for the forensic application of a basic set of 7 STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) for standard Y-haplotyping in forensic and paternity casework. We recommend further the inclusion of the highly polymorphic bilocal Y-STRs DYS385, YCAII, YCAIII for a nearly complete individualisation of almost any given unrelated male individual. Together, these results suggest that Y-STR loci are useful markers to identify males and male lineages in forensic practice. Received: 30 December 1996 / Received in revised form: 26 February 1997     

Pseudo-exclusion from paternity due to maternal uniparental disomy 16

The investigation of a case of disputed paternity revealed indirect exclusion of the alleged father in the haptoglobin system and in the DNA single-locus system D16S309/Hinf I (MS205). The paternity index for the non-exclusion systems was > 10⁶. Since both exclusion systems (HP and MS205) are located on chromosome 16, we investigated 10 microsatellite loci covering this chromosome with 10–20 cM resolution. Analysis of the child’s chromosome showed only alleles of maternal origin and lack of inheritance of paternal alleles for five informative loci. The markers close to the centromere of chromosome 16 were heterozygous, whereas distal loci were either heterozygous or homozygous for maternal alleles. This is consistent with a maternal meiosis I nondisjunction of chromosome 16 leading to maternal uniparental heterodisomy. This case emphasizes that the opinion of non-paternity should be based on the absence of paternal alleles at genetic systems located on at least two different chromosomes. Received: 23 December 1997 / Received in revised form: 9 February 1998     

Evaluation of the 124-plex SNP typing microarray for forensic testing

Human identification systems such as criminal databases, forensic DNA testing and genetic genealogy require reliable and cost-effective genotyping of autosomal, mitochondrial and Y chromosome markers from different biological materials, including venous blood and saliva. Although many such assays are available, few systems are capable of simultaneously detecting all three targets in a single reaction. Employing the APEX-2 principle, we have characterized a novel 124-plex assay, using specific primer extension, universal primer amplification and single base extension on an oligonucleotide array. The assay has been designed for simultaneous genotyping of SNPs from the single copy loci (46 autosomal and 29 Y chromosomal markers) side by side with SNPs from the mitochondrial genome (49 markers) that appears in up to thousands of copies per cell in certain tissue types. All the autosomal SNPs (from the SNPforID Consortium) included in the multiplex assay are unlinked and are distributed widely across autosomes, enabling genetic fingerprints to be distinguished. Mitochondrial DNA and Y chromosome polymorphisms that define haplogroups common in European populations are included to allow for maternity and paternity testing and for the analysis of genetic genealogies. After assay optimization we estimated the accuracy (99.83%) and call rate (99.66%) of the protocol on 17 mother–father–child/children families and five internal control DNAs. In addition, 79 unrelated Estonian and Swedish DNA samples were genotyped and the accuracy of mtDNA and Y chromosome haplogroup inference by the multiplex method was assessed using conventional genotyping methods and direct sequencing.     

Highly informative Y-chromosomal haplotypes by the addition of three new STRs DYS437, DYS438 and DYS439

The Y chromosome STRs DYS437, DYS438 and DYS439 were selected from publicly available genome databases and used to analyse an Italian population sample. A tetraplex PCR reaction including the highly informative DYS385 locus, was set up and used for the analysis of 131 male samples to determine allele frequencies and STR diversity values. The number of different haplotypes and the haplotype diversity value found from the analysis of the STRs included in the tetraplex reaction were very similar to those found from the analysis of the basic set of 7 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392 and DYS393) previously carried out on the same population sample. By combining the allelic states of the 11 Y-chromosomal STRs we could construct highly informative haplotypes that allowed the discrimination of 93.8% (120 out of 128) of the samples tested. This approach represents a very powerful tool for individual identification and paternity testing in forensic medicine. Received: 29 November 1999 / Accepted: 17 March 2000     

Population data on 6 short tandem repeat loci in a sample of Caucasian-Mestizos from Colombia

Blood samples from 409–452 unrelated Colombian Caucasian-Mestizo individuals were amplified and typed for six short tandem repeat (STR) markers (HUMF13A01, HUMFES/FPS, HUMVWA, HUMCSF1PO, HUMTPOX, HUMTH01). The allele frequencies, genotype frequencies, heterozygocity, mean paternity exclusion chance, polymorphism information content, discrimination power, assumption of independence within and between loci and Hardy Weinberg equilibrium were determined. The results demonstrate that all markers conform to Hardy-Weinberg equilibrium expectations. In addition, the results demonstrate the assumption of independence within and between the loci analysed. The mean exclusion chance (MEC) was 0.9851 for all six STR loci analysed and the discrimination power (DP) was 0.9999973. Therefore, this Colombian population database can be used in identity testing to estimate the frequency of a multiple PCR-based locus DNA profile in forensic cases as well as in paternity testing. Received: 24 September 1998 / Received in revised form: 22 December 1998 / Accepted: 11 January 1999     

Paternity evaluation in cases lacking a mother and nondetectable alleles

In parentage testing the formulae for computing paternity index and exclusion probability generally ignores the presence of nondetectable alleles at the loci tested. In contrast, it is now known that even when paternity testing is done with hypervariable DNA markers, nondetectable alleles should not be ignored. This work presents simple formulae needed with this consideration, to analyze paternity evaluation from DNA markers in cases where the mother of the disputed child is unavailable for testing. It is shown that even a modest frequency of nondetectable alleles (e.g., 2–5% per locus) may have a substantial impact on the paternity index when the child and/or the alleged father exhibits a single-banded DNA profile at a locus. Use of such formulae can generate a high probability of exclusion and a high paternity index when multiple independently segregating hypervariable DNA markers are used.     

Two additional reports of deletion on the short arm of the Y chromosome

Deletions on the short arm of the Y chromosome involving the amelogenin Y gene (AMELY), located on Yp11.2, can be misleading for sex typing with serious consequences in forensic applications and prenatal diagnosis. In this study, we describe two AMELY null cases concerning two unrelated Italian males from Northeast Italy. PCR amplification of short tandem repeats on the Y chromosome (Y-STRs) showed a lack of AMELY and DYS458 markers. The presence of all the other markers located on the Y chromosome and of the SRY gene in both samples led us to conclude that a deletion had occurred in a portion of the short arm of the Y chromosome. Twenty-three Y-specific sequence tagged sites (STSs) were chosen to delineate the deletion's length, which was estimated to be in the range of 3.35-3.87Mb for one sample and 1.51-2.58Mb for the other. These and previous findings suggest that in all cases where potential AMELY drop out has occurred, it should be used additional specific Y chromosome markers or human DNA quantification methods that specifically quantify male DNA using target male genomic markers, which not being located within the deletion regions, allow an accurate sex identification.     

Analysis of Y chromosome microdeletions and CFTR gene mutations as genetic markers of infertility in Serbian men

BACKGROUND/AIM: Impaired fertility of a male partner is the main cause of infertility in up to one half of all infertile couples. At the genetic level, male infertility can be caused by chromosome aberrations or gene mutations. The presence and types of Y chromosome microdeletions and cystic fybrosis transmembrane conductance regulator (CFTR) gene mutations as genetic cause of male infertility was tested in Serbian men. The aim of this study was to analyze CFTR gene mutations and Y chromosome microdelations as potential causes of male infertility in Serbian patients, as well as to test the hypothesis that CFTR mutations in infertile men are predominantly located in the several last exons of the gene. METHODS: This study has encompassed 33 men with oligo- or azoospermia. The screening for Y chromosome microdeletions in the azoospermia factor (AZF) region was performed by multiplex PCR analysis. The screening of the CFTR gene was performed by denaturing gradient gel electrophoresis (DGGE) method. RESULTS: Deletions on Y chromosome were detected in four patients, predominantly in AZFc region (four of total six deletions). Mutations in the CFTR gene were detected on eight out of 66 analyzed chromosomes of infertile men. The most common mutation was F508del (six of total eight mutations). CONCLUSION: This study confirmed that both Y chromosome microdeletions and CFTR gene mutations played important role in etiology of male infertility in Serbian infertile men. Genetic testing for Y chromosome microdeletions and CFTR gene mutations has been introduced in routine daignostics and offered to couples undergoing assisted reproduction techniques. Considering that both the type of Y chromosome microdeletion and the type of CFTR mutation have a prognostic value, it is recomended that AZF and CFTR genotyping should not only be performed in patients with reduced sperm quality before undergoing assisted reproduction, but also for the purpose of preimplantation and prenatal diagnostics in couples in which in vitro fertilization has been performed successfully.     

Lewis genotyping by the PCR-RFLP method in a Japanese population and its evaluation in forensic analysis

Lewis phenotyping of red blood cells has many problems such as the influence of many biological conditions, the change during the period from newborn to early childhood and mistyping by non-specific anti-Lewis antibodies. Therefore, it would be useful to determine the Lewis genotype. Recently a method of Le-genotyping by PCR-RFLP was established. We determined the frequencies of Lewis genotypes in a Japanese population and discuss the applicability to paternity tests and other forensic applications. The gene frequencies of Le, le1 and le2 in the Japanese population studied were 0.7032, 0.2358 and 0.0610 respectively. Out of 12 paternity cases where paternity was excluded by other markers, 3 alleged fathers could also be excluded by Lewis genotyping. The genotype from organs of a fetus from a 3-month pregnancy was Le/Le. The determination of Lewis genotypes could play a useful role as a genetic marker in paternity tests and forensic analyses. Received: 9 October 1996 / Received in revised form: 1 April 1997     

Genetic variability at nine STR loci in the Chueta (Majorcan Jews) and the Balearic populations investigated by a single multiplex reaction

A study of the genetic variability in the Chueta (Majorcan Jews) and the Balearic (Majorca and Minorca Islands) populations was carried out using a multiplex system containing the nine tetrameric STRs D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820. The Chueta population has remained isolated because intermarriage with non-Jews did not take place until the middle of this century, which has resulted in it being a small inbred community. The results indicate the existence of HW equilibrium for the Chueta and Balearic populations. No pair-wise correlation was observed between the nine markers. Consequently, they seem to comprise a suitable group of markers for population genetics purposes and for paternity and forensic testing. Received: 12 April 1999 / Received in revised form: 11 August 1999     

Y-Chromosome STR haplotypes in an Italian population sample

Seven Y-chromosome STRs were investigated in a male population sample from the Modena area by means of one quadruplex reaction (systems DYS19, DYS390, DYS391, DYS393), one duplex reaction (systems DYS389-II, DYS392) and two single PCR reactions (DXYS156 and DYS389-I/II). In 100 males, 71 different haplotypes could be observed, 57 of which were seen only once. The haplotype diversity/discrimination index is 0.97. The resulting database could be used for routine forensic application like paternity testing and stain investigation. Received: 6 November 1997 / Received in revised form: 12 March 1998     

Paternity testing using Y-STR haplotypes: assigning a probability for paternity in cases of mutations

In parentage testing with male children, Y-chromosomal STR evidence is gaining more and more importance. In some cases, multilocus haplotypes of related persons can differ at a single locus due to a mutation. In this work, a likelihood approach is presented for the calculation of a probability for paternity under consideration of a single mutation event on the Y-chromosome. The new methodology is applied to two case examples. Received: 10 April 2000 / Accepted: 2 December 2000     

Typing of Y chromosome single nucleotide polymorphisms in a Japanese population by a multiplexed single nucleotide primer extension reaction

We have developed a new method for typing single nucleotide polymorphisms (SNPs) on the human Y chromosome based on a multiplexed single nucleotide primer extension. This method has the advantage that several SNPs are typed rapidly and simultaneously. We examined 15 different SNP loci on Y chromosome, M9, M105, M122, M125, M128, M130, SRY465, IMS-JST006241, IMS-JST006841, IMS-JST002611, IMS-JST003305, IMS-JST008425, IMS-JST021354, IMS-JST021355 and IMS-JST055457, in 159 Japanese males. From the typing results of these 15 loci, we found 13 haplotypes. Gene diversity for each locus ranged from 0.025 to 0.486 and the haplotype diversity was estimated to be 0.838. This method could be readily applied for personal identification and paternity testing.     

Y chromosome polymorphisms and haplotypes in West Saxony (Germany)

In order to apply a set of useful and high polymorphic Y-STRs in paternity testing, we performed a population genetic study from Saxony. The allele distributions of the systems DYS19, DYS385, DYS389I/II and DYS390 were investigated in a sample of 250 unrelated males from the area of Leipzig. PCR products were detected using native polyacrylamide gel electrophoresis as well as capillary electrophoresis and GenScan Software on the ABI Prism 310 DNA sequencer. Haplotype frequency data of 164 different types were obtained which show that these four systems are very useful for special cases of paternity and forensic stain analysis. In addition several confirmed father-son pairs were examined using the paternity cases of the institute. One mutation was found in the system DYS390 and sequencing data are presented. Received:22 December 1997 / Received in revised form: 26 January 1998     

Resolving a 150-year-old paternity case in Mormon history using DTC autosomal DNA testing of distant relatives

Although autosomal DNA testing has been available for a number of years, its use to reconstruct genetic profiles of people that lived centuries in the past is relatively recent and there are no published cases where it was employed to verify a kinship relation, likely to be an alleged paternity, that occurred one and a half century ago.DNA testing has already been employed to study the ancestry and posterity of Joseph Smith Jr., founder of the Latter-day Saint (Mormon) movement. Thanks to information found on the paternally inherited Y chromosome, a number of alleged paternities have been disproved, but obviously this analysis is not effective for alleged daughters. Likewise, his reconstructed mitogenome sequence, reported here for the first time, provides information about his maternal ancestry, but is useless in any paternity questions due to the strict maternal inheritance. Among all the children attributed to Joseph Smith Jr., Josephine Lyon, born in 1844, is perhaps the most frequently mentioned.In the current study, 56 individuals, mostly direct descendants of Joseph Smith Jr. and Josephine Lyon, had their autosomal DNA tested to verify Josephine’s biological paternity. Nearly 600,000 autosomal SNPs from each subject were typed and detailed genealogical data were compiled. The absence of shared DNA between Josephine’s grandson and Joseph Smith Jr.’s five great-grandchildren together with various amounts of autosomal DNA shared by the same individual with four other relatives of Windsor Lyon is a clear indication that Josephine was not related to the Smith, but to the Lyon’s family. These inferences were also verified using kinship analyses and likelihood ratio calculations.     

Population genetics of the STRs vWA, D3S1358 and FGA in the Pomerania-Kujawy region of Poland

This paper presents the results of a Polish population study (n = 210) for the three STR loci vWA, D3S1358 and FGA analysed using the multiplex PCR system AmpflSTR Blue. The allele distributions were in accordance with Hardy-Weinberg expectations. The combined mean exclusion chance, mean paternity index and power of discrimination for the three loci were MEC = 0.96055, MPI = 127.1295 and PD = 0.99986. This demonstrates that these systems are valuable tools for forensic identification and paternity testing. Received: 24 August 1998 / Received in revised form: 19 January 1999     

Paternity testing after pregnancy termination using laser microdissection of chorionic villi

We report an unusual case of paternity testing from residues of chorionic villi 5 weeks after pregnancy termination. The autopsy of a 32-year-old female homicide victim revealed the presence of intact chorionic villi at the former placenta implantation site. Fetal cells were selectively isolated by laser-induced microdissection of the remaining villi to avoid contamination with maternal DNA. Simultaneous amplification of 12 STR loci in 2 PCR reactions resulted in a combined probability of paternity of 99.94%. This case demonstrates that laser-assisted microdissection and multiplex STR typing provide tools for paternity testing performed on endometrial mucosa long after the product of conception was removed by therapeutic abortion. Received: 2 May 2000 / Accepted: 7 November 2000     

Is the amelogenin gene reliable for gender identification in forensic casework and prenatal diagnosis?

In humans, the amelogenin gene is present on both the X and the Y chromosomes. However, there are size differences in this gene between these chromosomes, which have been utilised for sexing in forensic casework and prenatal diagnosis. Our study using the AmpFl STR Profiler Plus kit, showed a deletion of Y chromosome-specific amelogenin in five Indian males (1.85%). We propose to call them “deleted-amelogenin males” (DAMs), who but for the detection of the presence of other Y-specific markers (e.g. SRY, STR and 50f2) would have been identified as females. Considering the consequences of the result obtained only using the amelogenin marker, we suggest the use of additional Y chromosome markers for unambiguous gender identification. Received: 17 May 2001 / Accepted: 24 July 2001     

Assessing paternities with inconclusive STR results: The suitability of bi-allelic markers

In paternity testing the genetic profiles of the individuals are used to compare the relative likelihoods of the alleged father and the child being related as father/offspring against, usually, being unrelated.In the great majority of the cases, analyses with the widely used sets of short tandem repeat markers (STRs) provide powerful statistical evidence favouring one of the alternative hypotheses. Nevertheless, there are situations where the final statistical result is ambiguous, mostly because the alleged father shows incompatible genotypes at a few loci along with a very high paternity index in the remaining systems. In these cases, the possibility that the alleged father is actually a close relative of the real one (son, father or brother) can reasonably be raised.In such cases, when the statistical evidence obtained is considered as insufficient, the common practice is to extend the set of analysed markers. In this context, many authors have suggested that bi-allelic markers, such as single nucleotide (SNP) or insertion/deletion (Indel) polymorphisms, are markers of choice, as they are incomparably less prone to mutation than STRs.In this work we address the soundness of this claim and the consequences of this strategy, analyzing the a priori odds both for (a) expected number of Mendelian incompatibilities, and (b) expected values for the final likelihood ratios. Moreover, one hundred real pairs of second degree relatives, typed for two sets of markers: 15 STRs plus 38 Indels, were used to simulate paternity testing. Our data show that, for the number of markers commonly considered, the results from an extended battery of SNPs or Indels should be interpreted with caution when relatives are possibly involved.     

A case study of heteropaternal superfecundation in a pair of Chinese twins

A newly discovered case of heteropaternal superfecundation is reported. In a case of disputed paternity involving a pair of male twins, the results suggested that the twins had different biological fathers. Heteropaternal superfecundation is rarely observed among humans; our laboratory has encountered only one case of heteropaternal twins in 78 cases of twin disputed paternities. Therefore, when it comes to the paternity testing of dizygotic twins, the possibility of heteropaternity should be kept in mind.