Characterisation of variant alleles in the STR systems D2S1338, D3S1358 and D19S433

Comparison of massively parallel sequencing to capillary electrophoresis for short tandem repeat genotyping of trace DNA

In forensic genetics, massively parallel sequencing (MPS) offers several advantages over the current golden standard, capillary electrophoresis (CE): additional sequence information, shorter amplicon lengths, and the simultaneous analysis of many markers. These benefits result in a reduced number of reactions necessary while improving the amount of data obtained, thereby conserving valuable sample extracts. This proves particularly advantageous for the analysis of trace DNA. This study assessed the suitability of MPS for short tandem repeat (STR) typing of low template samples compared with results obtained through CE. The MPS genotypes showed higher concordance to reference genotypes, with donor alleles being more frequently assigned to be the major contributor, meeting the requirements for database entry. However, the MPS workflow is more time-consuming and associated with higher costs.

Flanking Variation Influences Rates of Stutter in Simple Repeats

It has been posited that the longest uninterrupted stretch (LUS) of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL). While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the PAL, examples to the contrary are apparent in commonly assayed forensic markers. Further, flanking variation that is 7 bp from the repeat region can impact rates of stutter. These findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers.

Elevated germline mutation rate in teenage fathers

Men age and die, while cells in their germline are programmed to be immortal. To elucidate how germ cells maintain viable DNA despite increasing parental age, we analysed DNA from 24 097 parents and their children, from Europe, the Middle East and Africa. We chose repetitive microsatellite DNA that mutates (unlike point mutations) only as a result of cellular replication, providing us with a natural ‘cell-cycle counter’. We observe, as expected, that the overall mutation rate for fathers is seven times higher than for mothers. Also as expected, mothers have a low and lifelong constant DNA mutation rate. Surprisingly, however, we discover that (i) teenage fathers already set out from a much higher mutation rate than teenage mothers (potentially equivalent to 77–196 male germline cell divisions by puberty); and (ii) ageing men maintain sperm DNA quality similar to that of teenagers, presumably by using fresh batches of stem cells known as ‘A-dark spermatogonia’.

Identification of the sequence variations of 15 autosomal STR loci in a Chinese population

BACKGROUND

DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected.

AIM

In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci.

SUBJECTS AND METHODS

Suspected null alleles and OL alleles of PlowerPlex16® System from 21,934 unrelated Chinese individuals were verified by alternative systems and sequenced.

RESULTS

A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751 × 10(-4). Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01.

CONCLUSION

Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.

Long allele designations at D2S1338 and D19S433 loci as influenced by various multiplex STR kits

European forensic laboratories are replacing the STR multiplex kits with the new generation 16/17 STR kits. This study examines the influence of the new generation kits and the new Applied Biosystems 3500xL Genetic Analyzer on the designation of long D2S1338 and D19S433 off-ladder alleles. Different allele calls were obtained using the new NGM™ (Applied Biosystems) and PowerPlex(®) ESI™ (Promega) kits compared with AmpFℓSTR(®) SGM Plus™ kit (Applied Biosystems). Sequence analysis was used to determine accurate allele designation. The new multiplex kits and the 3500xL Genetic Analyzer improved accuracy of long allele designations. DNA databases worldwide include countless profiles obtained by previous kits. Discrepancies between the new and former technologies may cause failure to detect hits. Discordance is expected due to primer sequence differences between various kits. An additional discordance, occurring in long alleles, independent of primer sequence is reported in this study.

Discordance at D3S1358 locus involving SGM Plus™ and the European new generation multiplex kits

During the course of routine database sample analysis in the Israel Police DNA database, an off-ladder D3S1358 allele, calculated to be >22.1, extending into the adjacent vWA locus was observed using Applied Biosystems SGM Plus™ kit. To verify the size of this D3S1358 long allele and to ensure it was not part of a trialle pattern in the neighboring locus, the sample was amplified using three of the European new generation STR multiplex kits: NGM(TM) (Applied Biosystem), Powerplex™ ESX and ESI (Promega). The results of these amplifications determined the variant to be a 22 allele. Subsequent sequencing confirmed this designation and revealed a nucleotide polymorphism. Ten additional SGM Plus™ profiled samples with D3S1358 alleles larger than 19, were re-analyzed using NGM(TM) and Powerplex™ ESX which also showed discordance in the calculated results between original SGM Plus™ designations and those obtained with the European new generation multiplexes.

STR sequence analysis for characterizing normal, variant, and null alleles

DNA sequence variation is known to exist in and around the repeat region of short tandem repeat (STR) loci used in human identity testing. While the vast majority of STR alleles measured in forensic DNA laboratories worldwide type as "normal" alleles compared with STR kit allelic ladders, a number of variant alleles have been reported. In addition, a sequence difference at a polymerase chain reaction (PCR) primer binding site in the DNA template can cause allele drop-out (i.e., a "null" or "silent" allele) with one set of primers and not with another. Our group at the National Institute of Standards and Technology (NIST) has been sequencing variant and null alleles supplied by forensic labs and cataloging this information on the NIST STRBase website for the past decade. The PCR primer sequences and strategy used for our STR allele sequencing work involving 23 autosomal STRs and 17 Y-chromosome STRs are described along with the results from 111 variant and 17 null alleles.

A D19S433 primer binding site mutation and the frequency in Japanese of the silent allele it causes

Short tandem repeat studies are powerful tools for parentage analysis and for identification of missing persons, victims of murder, and victims of mass fatalities when reference samples are unavailable. The primer in the Identifiler kit failed to amplify an allele at the D19S433 locus, producing a silent ("null") allele. The causal mutation is a base change (G>A) 32 nucleotides downstream from the 3' end of the AAGG repeats. The silent alleles are problematical in parentage analysis because when transmitted, they can cause a parent-child inconsistency that is unrelated to Mendelian genetics. The inconsistency is sometimes termed an "apparent opposite homozygosity" and it produces false evidence of nonparentage. Alternative primers were designed to amplify the D19S433 locus alleles and they detect the silent allele. Frequencies of the (no longer) silent allele were determined to be 0.0114 in 176 people from Shizuoka (Honshu) and 0.0128 in 156 people from Okinawa.

Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus and PowerPlex 16

During duplicate analysis of buccal swabs from 1,377 individuals with 2 commercial short tandem repeat (STR) kits, we observed 8 discordant phenotypes with SGM Plus (SGM, second generation multiplex) for the STRs THO1 (2), vWA (4) and D18S51 (2), and 1 discrepancy with PowerPlex 16 for D18S51. One individual even showed two discrepancies (vWA and THO1) for SGM Plus. In each case, the difference observed was due to the non-amplification or allele dropout of the second allele in a heterozygous genotype. Sequence analysis revealed each time the presence of a mutation that probably coincided with the primer-binding site. Primer-binding site mutations for vWA and D18S51 have been reported previously, while the mutation for THO1 (C-to-T substitution at position 1286 of GenBank sequence D00269) is reported here for the first time. While the frequency of these silent alleles remains low (0.58% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.

Meiosis study in a population sample from Afghanistan: allele frequencies and mutation rates of 16 STR loci

The 16 short tandem repeat systems D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820, ACTBP2, D2S1338, D16S539, D19S433, D21S11, D18S51 and D8S1179 were amplified in a population sample composed of 333 immigrants from Afghanistan. The 16 loci met Hardy-Weinberg expectations and possess a combined matching probability of 1 in 3.6 x 10(14) and a combined mean exclusion chance greater than 0.9996 in this Afghan population. Approximately 12,000 meiotic transfers were investigated and 19 mutations were observed in the repeat units of FGA (n=6), ACTBP2 (n=5), D3S1358 (n=2), D5S818 (n=2), D7S820 (n=2), VWA (n=1) and D8S1179 (n=1).