Retrofitting massively parallel sequencing (MPS) for HLA-DQA1 and polymarker (PM) in forensic casework

Genotype profiling has played a major role in forensics for decades. The technology for detection and discrimination has advanced substantially, from serology to DNA sequence analysis. Currently, there may be situations where there is a need for re-analysis of forensic DNA data that was produced using methodology that is no longer available. An example of this is the allele-specific oligonucleotide hybridization assays used in the 1990s. In the study presented herein, we have developed a multiplex system combining PCR and massively parallel sequencing (MPS) technologies to identify DNA polymorphisms. Our results are consistent with those found in the widely utilized AmpliType PM + DQA1 Amplification and Typing Kit originally marketed by Perkin Elmer. During the course of our studies, it became apparent that paralogous genes for two of the loci, GYPA and HBG2 (formerly HBGG), could have confounded the interpretation of the original assays, and we describe the technical solutions we developed to overcome ambiguity in genotype assignment. This study results in a novel resource enabling the re-analysis of DNA profiling results produced decades past using current day technology.

Targeted extended cystic fibrosis mutation testing on known and at-risk patients and relatives

This paper reports mathematically derived residual risks of being a carrier or being affected with cystic fibrosis following various screening scenarios to assist in interpreting test results and advising patients. While parental screening with 23 American College of Medical Genetics (ACMG) cystic fibrosis mutations defines the 64% of affected U.S. Caucasian fetuses with two detectable mutations, newborn screening for elevated immunoreactive trypsinogen (IRT) and sweat chloride identifies an additional 36% of affected newborns with zero or one detected mutation. The relatives of these affected newborns with less than two detectable mutations have higher posterior (after) 23 mutation-negative test risks of carrying undetected mutations. These calculations emphasize how knowledge of the mutations in the related affected patient substantially improves upon the quality of after-test advice to patients. Furthermore, negative tests of the partner without a family history and/or more extensive cystic fibrosis transmembrane conductance regulator (CFTR) gene testing also increases the likelihood that a negative report is truly negative. When a newborn patient with zero or one detected CFTR mutation has an inconclusive sweat test result, the sweat test should be repeated before ordering additional often unnecessary CFTR gene sequencing. Given the same composite mutation panel test accuracy, a higher proportion of reported test results would be correct during parental screening than when testing at-risk fetuses or symptomatic newborns. Prenatal and newborn screening would be enhanced substantially by medical professionals offering copies of all positive parental and newborn test reports to the parents to share with their relatives. These principles are likely to be applicable to other genetic diseases as the most common mutation frequencies are reported.

Chronic lung disease and cystic fibrosis phenotype in prolidase deficiency: a newly recognized association

Six families with prolidase deficiency (PD) and chronic lung disease are reported, a previously unrecognized association. In one family with a classic cystic fibrosis (CF) phenotype, no evidence for CF Transmembrane Conductance Regulator (CFTR)-related mutations could be found. Chronic lung disease and CFTR-mutation negative CF may be associated with PD.

Genetic population history relationships of the population of Bogotá, Colombia, by using the D1S80, VWA, and TH01 molecular markers

The genetic relationships of the population of Bogotá, Colombia, was comparatively studied with regard to other populations from America, Europe, and Asia, by using the D1S80, VWA, and TH01 molecular loci. From a population history point of view, the population of Bogotá seems to be more related to a European origin, with several differential contributions coming from Amerindians rather than from African and Asian populations, when the D1S80 and TH01 markers were employed. However, the contribution was greater from African populations for the VWA marker. Several explanations are offered to resolve the genetic affiliation of this population.

Association between LDLR polymorphism and diseases in the Japanese population: aging and distribution of the polymorphism

A number of DNA polymorphisms have been found to be associated with the pathophysiology of some common disease. If the LDLR polymorphism is directly or indirectly related to some fatal disease, the distribution of the polymorphism may vary with age. We therefore investigated the aging-associated distribution of the LDLR polymorphism. Blood samples were collected from Japanese cadavers (aged 0-91) at autopsy. The LDLR polymorphism was detected using a AmpliType PM PCR Typing kit. When the LDLR genotype was examined in cadavers divided according to age into 0-29 year group, 30-59 year group, and 60-91 year group, there were significant differences in genotype among the three age groups and between the 0-29 year group and 60-91 year group. The LDLR-A genotype tended to be lower in the older cadavers. The present study revealed that there were aging-dependent differences in the distribution of the LDLR polymorphism in autopsy samples, suggesting that a common mutation involved in the occurrence of fatal diseases may be present near the LDLR-A polymorphism locus.

Jordanian population data on the PCR-based loci: LDLR, GYPA, HBGG, D7S8 and GC

Genotype and allele frequency distributions for PM polymerase chain reaction (PCR)-based genetic markers were determined in a Jordanian sample population. Results were obtained using the AmpliType PM PCR Amplification and typing kit. All loci were in agreement with the Hardy-Weinberg equilibrium expectations. The predominant alleles for LDLR, GYPA, HBGG, D7S8 and GC loci were B, A, B, A and C respectively. No statistically significant variation was detected in allele frequencies of these loci in Jordanians compared to that in Israeli Arab, U.S Caucasian and Japanese populations. Data presented here can be used to estimate the frequency of a specific DNA profile in the Jordanian population for forensic analyses and paternity testing.

Donor origin of a posttransplant liver allograft malignancy identified by fluorescence in situ hybridization for the Y chromosome and DNA genotyping

Posttransplantation malignancy in the allograft is a rare complication of orthotopic liver transplantation. In the described case, an abnormal T-tube cholangiogram, performed 6 months after orthotopic liver transplantation between a male donor and a female recipient, prompted needle liver biopsy. A moderately differentiated adenocarcinoma was found. Fluorescence in situ hybridization for the Y chromosome indicated male origin of malignancy. Donor-related disease was confirmed by comparative DNA analysis of genomic sequences from the donor liver, associated tumor, and recipient peripheral blood. Results of these investigations qualified the recipient for a second liver transplant.

Frequencies of the five PCR-based genetic markers LDLR, GYPA, HBGG, D7S8 and GC in the population of Asturias (North Spain)

Allele and genotype frequencies of the loci LDLR, GYPA, HBGG, D7S8 and GC (PM loci) were investigated in a population sample of 215 unrelated individuals from Asturias (North Spain). Multiplex amplification and simultaneous typing of the five loci was carried out using the polymarker PCR amplification and typing kit. All loci met Hardy-Weinberg expectations. The Asturian sample does not differ significantly from other Caucasians, but significant differences were observed between this population and SW Hispanic, Afro-american and Korean populations.

Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci

In order that there can be confidence that DNA profile frequency estimates will not place undue bias against a defendant, 2 methods are described for estimating minimum allele frequency bounds for PCR-based loci. One approach estimates minimum allele frequencies for VNTR and STR loci using sample size and the observed heterozygosity at a locus, while the second approach, appropriate for loci typed with allele-specific oligonucleotide probes, is based only on sample size. The use of a minimum allele frequency enables compensation for sparse sampling of infrequent alleles in population databases.

Italian population data on the loci LDLR, GYPA, HBGG, D7S8 and GC

Allele and genotype frequencies for the five loci LDLR, GYPA, HBGG, D7S8 and GC were determined for 374 unrelated Italians using a multiplex PCR-amplification and typing commercial kit. The distribution of the genotype frequencies showed no deviations from Hardy-Weinberg expectations. The combined power of discrimination and chance of exclusion for all five loci were 0.999 and 0.702, respectively. A test for homogeneity was performed and no significant differences were observed among the Caucasian population samples.

Population data on the PCR-based loci LDLR GYPA, HBGG, D7S8, Gc, HLA-DQA1, and D1S80 from Arabs from Dubai

Population data were generated for the loci LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, and D1S80 from 180 Arabs from Dubai. Except for D7S8 (P = 0.003), the genotype frequency distributions for the loci do not deviate from Hardy Weinberg expectations. There was no evidence for departures from expectations of independence between the loci. Using a test for homogeneity, the loci LDLR, GYPA, D7S8, and Gc were similar between the Dubaian Arab population sample and an Arab population sample from Palestine and the occupied territories, while the loci HBGG (P = 0.003), DQA1 (P < 10(-3)), and D1S80 (P = 0.020) were statistically different.

The effects of inbreeding on DNA profile frequency estimates using PCR-based loci

Estimates of inbreeding were determined using Wright's FST for loci used for PCR-based forensic analyses. The populations analyzed were African Americans, Caucasians, Hispanics, and Orientals. In most cases the FST values at each locus were less than 0.01. The FST values over all loci for African Americans, Caucasians, and Orientals ranged from 0.0015 to 0.0048. No substantial differences were observed for DNA profile frequency estimates when calculated under the assumption of independence or with the incorporation of FST.

Amplification of the MET gene in glioma

We have previously reported the finding of MET amplification linked to double minutes (dmins) in a human glioblastoma (TX3095). Because dmins are found in approximately 50% of glioblastomas, 18 gliomas were analyzed for MET amplification. Three grade IV glioblastomas and one grade II astrocytoma showed amplification. We could also localize the MET amplicon to dmins in glioblastoma TX3095 by fluorescence in situ hybridization.

Pancreatic insufficiency and pulmonary disease in German and Slavic cystic fibrosis patients with the R347P mutation

Cystic fibrosis (CF) is caused by mutations in the gene for the cystic fibrosis transmembrane conductance regulator (CFTR) that codes for a cAMP-regulated chloride channel. The R347P is a missense mutation located within the first membrane spanning domain (MSD1) of the CFTR protein. This mutation occurs with an overall worldwide frequency of about 0.2%. The patients, originally described with this mutation were compound heterozygotes with the delta F508 mutation and had a very mild course of CF, suggesting that R347P, similar to other missense mutations affecting the MSD1 domain, causes a mild phenotype. We report here a group of 19 CF patients with the R347P mutation of German, Bulgarian, Czech, and Slovak origin, including two homozygotes. Most patients presented with early disease onset, pancreas insufficiency (PI), and early pulmonary involvement, suggesting that this mutation can lead to a severe course of CF. Most R347P alleles in the group studied share a common polymorphic haplotype. In addition, these analyses gave evidence for recurrence of the mutation in two CF patients of German and Czech origin.

Dutch Caucasian population data on the loci LDLR, GYPA, HBGG, D7S8, and GC

To introduce the loci LDLR, GYPA, HBGG, D7S8, and GC (PM loci) in Dutch forensic identity testing, allele and genotype frequencies were determined in a Dutch Caucasian population sample, which had previously been typed for the HLADQA1 locus [12]. All 6 loci met Hardy-Weinberg equilibrium expectations, and there is little evidence for association between pairs of loci. The combined power of discrimination for all 6 loci is 0.9997. The allele frequencies of the PM loci were similar to 2 other Caucasian populations [3, 10], and differed from 3 non-Caucasian populations [3].

Swiss population data on the loci HLA-DQ alpha, LDLR, GYPA, HBGG, D7S8, Gc and D1S80

Allele and genotype frequencies for seven polymerase chain reaction-based DNA genetic markers were determined in a Swiss sample population. The loci are D1S80, HLA-DQ alpha, low density lipoprotein receptor, glycophorin A, hemoglobin G gammaglobin, D7S8, and group-specific component. All loci meet Hardy-Weinberg expectations. In addition, there is no detectable association of alleles between loci. The frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a DNA profile in the Swiss population.

Cystic fibrosis patients from the Black Sea region: the 1677delTA mutation

A 2 bp deletion in exon 10 of the CFTR gene, 1677delTA, which is very rare among CF chromosomes worldwide, was found to be a relatively common cause of cystic fibrosis in countries located in the region of the Black Sea. The frequency of the mutation was compared among cystic fibrosis patients from several populations, namely Bulgarians, Turks, Greek-Cypriots, Georgians, and Russians. The deletion is most common among Georgian CF patients and gradually declines in frequency in neighbouring populations. It is invariably related to a common polymorphic haplotype which is rare among normal chromosomes in Bulgaria but was found to be common in Turkey. The geographic gradient in the frequency of the mutation, along with findings on polymorphic haplotype distribution, suggest that the mutation is relatively young in evolutionary terms and spread as the result of west and south-bound migrations originating from Georgia. The 1677delTA mutation is related to a severe clinical phenotype with a high early mortality rate among homozygotes and possibly to an increased risk of meconium ileus.

A mutation in CFTR produces different phenotypes depending on chromosomal background

Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene but the association between mutation (genotype) and disease presentation (phenotype) is not straightforward. We have been investigating whether variants in the CFTR gene that alter splicing efficiency of exon 9 can affect the phenotype produced by a mutation. A missense mutation, R117H, which has been observed in three phenotypes, was found to occur on two chromosome backgrounds with intron 8 variants that have profoundly different effects upon splicing efficiency. A close association is shown between chromosome background of the R117H mutation and phenotype. These findings demonstrate that the genetic context in which a mutation occurs can play a significant role in determining the type of illness produced.

Intra- and extragenic marker haplotypes of CFTR mutations in cystic fibrosis families

In order to facilitate the screening for the less common mutations in the cystic fibrosis (CF) gene viz., the CF transmembrane conductance regulator gene (CFTR), marker haplotypes were determined for German non-CF (N) and CF chromosomes by polymerase chain reaction analysis of four polymorphisms upstream of the CF gene (XV-2c, KM.19, MP6-D9, J44) and six intragenic polymorphisms (GATT, TUB9, M470V, T854T, TUB18, TUB20) that span the CFTR gene from exon 6 through exon 21. Novel informative sequence variants of CFTR were detected in front of exons 10 (1525-61 A or G), 19 (3601-65 C or A), and 21 (4006-200 A or G). The CF locus exhibits strong long-range marker-marker linkage disequilibrium with breakpoints of recombination between XV-2c and KM.19, and between exons 10 and 19 of CFTR. Marker alleles of GATT-TUB9 and TUB18-TUB20 were found to be in absolute linkage disequilibrium. Four major haplotypes encompass more than 90% of German N and CF chromosomes. Fifteen CFTR mutations detected on 421 out of 500 CF chromosomes were each identified on one of these four predominant 7-marker haplotypes. Whereas all analysed delta F508 chromosomes carried the same KM.19-D9-J44-GATT-TUB9-M470V-T854T haplotype, another frequent mutation in Germany, R553X, was identified on two different major haplotypes. Hence, a priori haplotyping cannot exclude a particular CF mutation, but in combination with population genetic data, enables mutations to be ranked by decreasing probability.

A cystic fibrosis allele encoding missense mutations in both nucleotide binding folds of the cystic fibrosis transmembrane conductance regulator

German cystic fibrosis (CF) chromosomes were screened for molecular lesions in exon 20 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene by chemical cleavage of mismatch. An 3884G-to-A transition was detected in two patients which leads to an exchange of a serine by an asparagine in the Walker motif A of the second nucleotide binding fold. The affected serine residue is evolutionarily strongly conserved among the pro- and eukaryotic members of the protein superfamily of traffic ATPases. The two S1251N alleles were linked to the benign missense mutation F508C which is located in another conserved region of CFTR, the center region of the first nucleotide binding fold. Both patients with the complex allele F508C-S1251N are carrying delta F508 on the other CF chromosome and are suffering from severe pulmonary and gastrointestinal CF disease. Although F508C has been classified as a neutral sequence variation because of its discovery in healthy delta F508 gene carriers, it may nevertheless influence CFTR dysfunction caused by the S1251N mutation.