Are rapidly mutating Y-short tandem repeats useful to resolve a lineage? Expanding mutability data on distant male relationships.

BACKGROUND: Y-chromosomal short tandem repeats (Y-STRs) are essential to relate male lineages in forensic and evolutionary studies. Although large panels of Y-STR markers are now available, none possess sufficient discrimination power to distinguish close male relatives. This limit may be overcome by the use of rapidly mutating Y-STRs (RM Y-STRs), characterized by mutation rates higher than common Y-STRs. Recently, multicenter studies evaluated the ability of RM Y-STRs to differentiate father-son pairs; however, more extensive data on distantly related males are needed. STUDY DESIGN AND METHOD: A total of 157 male relative pairs separated by two to seven meiotic events, originating from Italy, were analyzed by 13 RM Y-STRs and 23 Y-STRs. RESULTS: Overall, 154 mutational events were observed at RM Y-STR loci and the estimated mutation rate was of 2.59 × 10(-2) (95% confidence interval, 2.16 × 10(-2) -2.97 × 10(-2) ). A total of 105 male relative pairs showed at least one mutation in at least one locus and differentiation rates increased from 52.8% to 88.9% from the second to the fourth generation, while 23 Y-STRs provided much lower values, spanning from 10.1% to 29.6%. CONCLUSIONS: These findings confirmed the higher capability of RM Y-STRs than conventional Y-STRs to resolve male lineages, thus suggesting a possible future use for forensic male individual identification.

Kinship analysis: assessment of related vs unrelated based on defined pedigrees.

The study aimed at evaluating whether the adoption of enlarged batteries of STR markers in kinship analysis may provide LR values suitable for discrimination of relatives from non-relatives, in comparison to conventionally used STR panels. The presence of LD among some loci and its effects on LR values were also assessed. Three hundred pairs of related and unrelated individuals, each separated from 1-3 generations and residing in North Italy were genotyped with the Investigator HDplex STR kit (Qiagen), AmpFlSTR Identifiler (Applied Biosystems), and PowerPlex Fusion System (Promega). Loci and alleles shared between each pair and within groups of relatives were compared. Also, combined LR values with and without loci in LD, sensitivity and specificity were calculated for each commercial kit and their combinations. Full siblings displayed the largest number of shared loci and alleles, with a proportion of LR ≥ 10 results significantly higher than other degrees of relatedness and, consequently, with the lowest percentage of inconclusive and false negative results. Only minor differences were detected in the combined LR distributions, after including or omitting loci in LD. However, these became only appreciable when analyzing more distant relative pairs.The implementation of additional STRs into the LR calculation allowed a complete and robust discrimination between relatives and non-relatives only for full siblings, by removing the typical uncertainty of the "grey zone", while this was not achieved among other degrees of relatedness. Furthermore, the presence of loci in LD seems to not significantly affect LR distributions within each generation.

Investigator HDplex markers: allele frequencies and mutational events in a North Italian population.

Autosomal short tandem repeats (STRs) analysis represents the method of election in forensic genetics and up to now, 23 STRs are available for these purposes. However, in particular circumstances such as human identification or complex kinship cases, examination of additional STRs may be required in order to obtain reliable conclusions. For this purpose, a new multiplex STR system, namely Investigator® HDplex kit (QIAGEN) that coamplifies a set of 12 autosomal loci, 9 of which, represents novel supplementary STRs, was recently developed. A population sample of 359 unrelated healthy subjects residing in North Italy was typed to determine allele frequencies, forensic parameters and genetic distances among European populations. Furthermore, to evaluate the suitability of the HDplex kit as an auxiliary tool for paternity testing, mutation rates were estimated on 84 confirmed family trios. The 12 loci resulted highly informative with a combined power of discrimination of 0.999998 and no departures from Hardy-Weinberg equilibrium were observed with the sole exception of locus D4S2366. From the comparison of our population sample and European reference populations, a single significant difference was revealed with the Poland population at D4S2366 locus. With regard to the mutation rate study, on a total of 2,016 meioses considered, six single-step mutational events were observed and the average mutation rate calculated was of 2.94 × 10(-3) per locus per generation (95% confidence interval, 1.08 × 10(-3)-6.39 × 10(-3)).

Haplotype data and mutation rates for the 23 Y-STR loci of PowerPlex® Y 23 System in a Northeast Italian population sample.

The PowerPlex® Y 23 System (Promega) is a short tandem repeat (STR) multiplex that allows co-amplification of 23 gonosomal Y-STRs, combining 17 loci commonly included in commercially available kits (DYS389I, DYS448, DYS389II, DYS19, DYS391, DYS438, DYS437, DYS635, DYS390, DYS439, DYS392, DYS393, DYS458, DYS385a/b, DYS456, and Y-GATA-H4) and six new loci (DYS481, DYS549, DYS533, DYS643, DYS576, and DYS570) with the last two being rapidly mutating Y-STRs (RM Y-STRs). In order to assess the possible gain in forensic efficiency provided by the six additional markers, a population sample of 410 unrelated healthy males originating from Northeast Italy (Veneto, Trentino Alto Adige, Lombardia, and Friuli Venezia Giulia regions) was typed. The data (335 of the 410 samples) are available in the Y chromosome haplotype reference database under accession number YA003327. Overall, 410 unique haplotypes were found corresponding to a global haplotype diversity (HD) of 0.999994 with a discriminatory capacity (DC) of 100%. Allelic microvariants, null alleles, and duplications were detected. Pairwise genetic distances (R(ST)) calculated among neighboring European reference populations revealed no significant differences. Furthermore, for studying Y-STR mutation rates, 90 father-son pairs, in which the fathers were already included in the full dataset, were tested. On a total of 2,070 meioses considered, eight single-step mutational events were observed, two of which within the same father-son pair and the average mutation rate was 3.38 × 10(-3) per locus per generation (95% confidence interval, 1.36 × 10(-3)-6.95 × 10(-3)).

Deletion and duplication at DYS448 and DYS626 loci: unexpected patterns within the AZFc region of the Y-chromosome.

Increasing the knowledge of multiple and microstructural events within the Y-chromosome may prove useful to better characterize abnormal short tandem repeats patterns complicating DNA profile interpretation. On the long arm of the human Y-chromosome, such structural rearrangements were observed in azoospermia factor regions (AZFa, AZFb, AZFc) that play an important role in male fertility and also host Y-STRs commonly used in forensic genetics. Here, we describe two cases, involving two males formerly included in an Italian population study, where DYS448 and DYS626 loci, located within the AZFc region, simultaneously displayed a double deletion in one case and a double duplication in the other. With the aim of better defining the size of both events, low and high-resolution mapping by means of 16 sequence-tagged sites was performed, and unexpected discontinued patterns within the palindromic segments b1/b3 of the AZFc were identified. Extending the analysis to their respective male relatives revealed unaltered transmission of the patterns along the two pedigrees. Reviewing literature data describing DYS448-DYS626 deletion and duplication suggested no close correlation between the occurrence of multiple/microstructural events and geographical origin.

FAF1, a gene that is disrupted in cleft palate and has conserved function in zebrafish.

Cranial neural crest (CNC) is a multipotent migratory cell population that gives rise to most of the craniofacial bones. An intricate network mediates CNC formation, epithelial-mesenchymal transition, migration along distinct paths, and differentiation. Errors in these processes lead to craniofacial abnormalities, including cleft lip and palate. Clefts are the most common congenital craniofacial defects. Patients have complications with feeding, speech, hearing, and dental and psychological development. Affected by both genetic predisposition and environmental factors, the complex etiology of clefts remains largely unknown. Here we show that Fas-associated factor-1 (FAF1) is disrupted and that its expression is decreased in a Pierre Robin family with an inherited translocation. Furthermore, the locus is strongly associated with cleft palate and shows an increased relative risk. Expression studies show that faf1 is highly expressed in zebrafish cartilages during embryogenesis. Knockdown of zebrafish faf1 leads to pharyngeal cartilage defects and jaw abnormality as a result of a failure of CNC to differentiate into and express cartilage-specific markers, such as sox9a and col2a1. Administration of faf1 mRNA rescues this phenotype. Our findings therefore identify FAF1 as a regulator of CNC differentiation and show that it predisposes humans to cleft palate and is necessary for lower jaw development in zebrafish.

Evaluation of genetic parameters of 22 autosomal STR loci (PowerPlex® Fusion System) in a population sample from Northern Italy.

The PowerPlex® Fusion System (Promega, Madison, WI) is a short tandem repeat (STR) multiplex that allows co-amplification of 22 autosomal STRs, including the CODIS core and the European Standard Set loci, plus amelogenin for gender determination and DYS391 male specific marker included in order to avoid errors in gender assignment when null Y-alleles or deletions of the Y-chromosome short arm involve the amelogenin locus. Allele frequencies and forensic efficiency parameters were estimated in a population sample of 303 unrelated healthy individuals living in Northern Italy. No significant deviations from Hardy-Weinberg expectations were observed after applying Bonferroni's correction for multiple testing. The combined power of discrimination was 0.999999999999 and the combined power of exclusion was 0.9999956. A rare 28 allele at locus D12S391 was observed, while one tri-allelic pattern at Penta E locus was detected. Population differentiation test revealed significant genetic diversity between our population sample and other European populations considered. The results showed that the PowerPlex® Fusion System is one of the most informative kit available in forensic genetics and may prove useful in both human identification and kinship analysis.

Short occupational exposure to glyphosate and its biomonitoring via urinary levels of glyphosate and metabolite AMPA (Amino-MethylPhosphonic acid), in Italian vineyard workers.

Glyphosate, an herbicide largely used in various contexts, can have adverse effects on human health. Although it is currently the most applied pesticide worldwide, few studies evaluated the extent of human exposure via biomonitoring. To expand such information, biological monitoring of exposure to glyphosate was conducted. The study has a before-and-after design to demonstrate the immediate impact of short-term interventions. Accordingly, the urine concentrations of glyphosate and its main biodegradation product (amino-methylphosphonic acid- AMPA) were measured before and the day after the single herbicide application in 17 male winegrowers. Urine samples were analyzed by high performance liquid chromatography coupled with a triple quadrupole mass spectrometer equipped with an electrospray ionization source. Glyphosate and AMPA were not detectable in pre-application urine samples (limit of quantification for glyphosate (LOQG) was 0.1 µg/L; limit of quantification for AMPA (LOQAMPA) was 0.5 µg/L). After application, glyphosate urinary levels were above LOQG in all workers. The median, min, and max values were 2.30, 0.51, and 47.2 µg/L, respectively. The same values were found for 50 %, 5 % and 95 % percentiles. After assigning numerical values, such as one half the LOQ, to each of the non-detects, the "z" of Wilcoxon matched-pairs signed-ranks test was -3.62 (p = 0.0003), suggesting the pre-application values being significantly lower than the post-application urinary glyphosate concentration. A similar analysis was not feasible with AMPA urinary levels, which were detectable only in 3 workers, after application. 12 (71 %) workers were significantly exposed to glyphosate, but adherence to the adoption of personal protective equipment was good: 14 (82 %) workers used gloves, 13 (76 %) used overalls and 13 (76 %) facial masks. Our data show that glyphosate can be absorbed by the workers after a single application and confirms the usefulness of biomonitoring in exposed workers. Further studies are needed in larger working populations and with multiple glyphosate applications, as well as to evaluate the correlations of glyphosate urine levels with exposure questionnaire data, in order to assess the actual relevance of risk and protection factors.

Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate.

We conducted a genome-wide association study for nonsyndromic cleft lip with or without cleft palate (NSCL/P) in 401 affected individuals and 1,323 controls, with replication in an independent sample of 793 NSCL/P triads. We report two new loci associated with NSCL/P at 17q22 (rs227731, combined P = 1.07 x 10(-8), relative risk in homozygotes = 1.84, 95% CI 1.34-2.53) and 10q25.3 (rs7078160, combined P = 1.92 x 10(-8), relative risk in homozygotes = 2.17, 95% CI 1.32-3.56).

Cutoff values for bacteria and leukocytes for urine flow cytometer Sysmex UF-1000i in urinary tract infections.

Because urinary tract infections (UTIs) are a quite common disease, the gold standard for diagnosing UTIs is still bacterial culture, although a large percentage of samples are negative: unnecessary cultures can be reduced by means of an effective screening test. The analytic performance of a new urine cytometer, the UF-1000i, has been tested on 1463 urine samples submitted to our laboratory for culture. Bacteria and leukocyte counts have been compared by means of the UF-1000i with colony-forming unit (CFU) quantification on citrate lactose electrolytes deficient agar to assess the best cutoff values. By using quantitative cultures and considering as positive a sample with 10 x 10(5) CFU/mL, 546 positive samples (37%) were observed. If compared with 10 x 10(5) CFU/mL, the cutoff values obtained were 125 bacteria/microL and 40 leukocytes/ microL, respectively. Analytic parameters such as sensitivity, specificity, positive predictive value, negative predictive value, and correctly classified incidence were satisfactory. Based on the results obtained in this study, when using the UF-1000i analyzer for a screening test for UTI, a cutoff value of 40 white blood cells/microL should be adopted. The cutoff value for bacteria should be 125/microL for those clinical conditions in which 10 x 10(5) CFU/mL indicates a positivity.

Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24.

We conducted a genome-wide association study involving 224 cases and 383 controls of Central European origin to identify susceptibility loci for nonsyndromic cleft lip with or without cleft palate (NSCL/P). A 640-kb region at chromosome 8q24.21 was found to contain multiple markers with highly significant evidence for association with the cleft phenotype, including three markers that reached genome-wide significance. The 640-kb cleft-associated region was saturated with 146 SNP markers and then analyzed in our entire NSCL/P sample of 462 unrelated cases and 954 controls. In the entire sample, the most significant SNP (rs987525) had a P value of 3.34 x 10(-24). The odds ratio was 2.57 (95% CI = 2.02-3.26) for the heterozygous genotype and 6.05 (95% CI = 3.88-9.43) for the homozygous genotype. The calculated population attributable risk for this marker is 0.41, suggesting that this study has identified a major susceptibility locus for NSCL/P.