Two examples of null alleles at the D19S433 locus due to the same 4 bp deletion in the presumptive primer binding site of the AmpFlSTR Identifiler kit

Two cases of allelic loss at the D19S433 locus after multiplex PCR with the AmpFlSTR Identifiler kit (Applied Biosystems) are described. In both cases the failure of PCR resulted in genetic inconsistencies due to opposite homozygosity. After singleplex PCR with published primers additional alleles were observed and Mendelian inheritance was restored. These PCR products were sequenced and in both cases the same 4 bp deletion near the 3′ end of the repeat region was detected in two alleles of different length. The frequency of these null alleles (two events in 1026 allelic transfers) amounts to 0.0019 (95% confidence limits: 0.0002-0.0070).     

Molecular characterization of a null allele at locus DXS8378

Typing of X-chromosomal short tandem repeat (STR) loci in a deficiency paternity case revealed a single Mendelian incompatibility between a female child and her putative grandmother, consisting of an opposite homozygosity at locus DXS8378. The presence of a null allele due to a primer binding site mutation on the child's paternally inherited X chromosome was confirmed by amplification with newly designed DXS8378 external primers. Sequencing analysis showed a point mutation (C > T transition at position 168, according to GenBank accession G08098) in the binding site of the original DXS8378 reverse primer.     

Null allele can bring to interpretative problems in a deficitary paternity case

An STR null allele is an allele at a microsatellite locus that fails to amplify. A possible cause is poor primer annealing due to nucleotide sequence divergence in the flanking primers. In this study, a woman (ZAM) wanted to know whether a man (PGAF) was the father of her child (ZGC). During the court settlement, PGAF died. PGAF’s parents refused to undergo DNA investigation and denied the access to biological fragments from their dead son. Although, DNA specimens were obtained from buccal swabs of ZAM, ZGC and PGAF’s paternal sister (PTFS). Initially, only autosomal profiles were studied, and kinship assignment was inconclusive. Following our requests, PGAF’s parents (PRGF and LLGM) led us to obtain their DNA specimens. Only with the PTFS genetic profile, we were not able to demonstrate a kinship assignment. PTFS showed a homozygosis at D8S1179 locus. Then, merely comparing PTFS, LLGM and ZGC autosomal genetic profiles it was possible to underline that they were three different homozygous at D8S1179 locus. Hence, comparing the peak heights in different loci and according to literature, they had to carry a null allele at this locus. Parental studies were completed by Y haplotype analysis.     

Large-scale concordance study for 16 autosomal STRs analyzed with PowerPlex ESI17 and NGM SElect

This study aimed at identifying the frequency of kit-dependent discordances and genetic specialties in STR DNA typing, which is particularly important for the interpretation of DNA profiles as well as national and international database searches. We analyzed a total of 27′510 buccal swabs with the PowerPlex ESI 17 and NGM SElect amplification kits and documented discordances and other anomalies. We found kit-dependent full dropouts to be the most frequent events, most of which were associated with the NGM SElect kit. The total kit-dependent discordance rate determined in this study amounts to 0.74%. With this dataset, we also provide dropout rates, which can be used to estimate silent allele frequencies for 16 common STR loci amplified with the PowerPlex ESI17 and NGM SElect amplification kits.     

Probabilistic expert systems for handling artifacts in complex DNA mixtures

This paper presents a coherent probabilistic framework for taking account of allelic dropout, stutter bands and silent alleles when interpreting STR DNA profiles from a mixture sample using peak size information arising from a PCR analysis. This information can be exploited for evaluating the evidential strength for a hypothesis that DNA from a particular person is present in the mixture. It extends an earlier Bayesian network approach that ignored such artifacts. We illustrate the use of the extended network on a published casework example.     

Powerplex® Y 23 System: Molecular characterization of a null allele at locus DYS549

We observed a null allele pattern at locus DYS549 in a male subject from North-East Italy typed with the PowerPlex^® Y 23 System (Promega). To investigate whether this pattern was due to the presence of a microdeletion/mutation in primer binding sites or in the locus target region, the sample was amplified with our designed DYS549 primers obtained from GenBank sequence (GDB: 515022). After amplification, a normal hemizygous genotype at this locus was generated, thus indicating the presence of a point mutation in the binding site of the original primer set of PowerPlex^® Y 23 System (Promega). This was further confirmed by sequence analysis, carried out with the Big Dye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems), according to the manufacturer's instructions. Sequences were run on the ABI Prism 3130 Genetic Analyzer (Applied Biosystems) and analyzed using the Sequencing Analysis v.5.3.1 and the SeqScape v2.6 softwares (Applied Biosystems). Ascertainment of the frequency of null alleles generated from variations at primer binding sites of short tandem repeats loci is of great importance in forensic genetics.     

中国成都地区汉族群体5个STR基因座的遗传多态性

采用PCR扩增,聚丙烯酰胺凝胶电泳分析技术,调查中国成都汉族群体DIS1656、D851179、D9S302、D185535及D195253等5个STR基因座的等位基因频率分布。D1S1656检出11个等位基因,35种基因型;DSS1179检出9个等位基因,32种基因型;D95302检出12个等位基因,50种基因型;D185535检出7个等位基因,20种基因型;D195253检出8个等位基因,28种基因型。5个STR基因座基因型频率分布符合Hardy-weinberg平衡（P＞0．05）。个人识别机率（DP）为0．92～0．98。分析了二代3口之家的遗传模式,证明5个STR基因座均符合孟德尔遗传规律。5个STR基因座PCR扩增采用同一条件,方法简单、快速、灵敏、重复性好,可用于法科学亲子鉴定和个人识别。     

A DYS438 null allele observed in two generations of a large family

Typing of Y-chromosomal STR loci using the AmpFISTR^® Yfiler kit showed a DNA profile lacking the DYS438 allele in an Austrian Caucasoid brother pair.Buccal swabs were collected from additional males of two generations and different branches of the family. All family members investigated did not show a DYS438 allele in their Yfiler profile. Using the Powerplex^® Y system an allele with dramatically reduced peak height was amplified. Subsequent sequencing of the DYS438 locus exhibited a transition upstream of the repetitive region.     

应用常染色体STR基因座共有等位基因数判别全同胞关系

目的建立基于常染色体STR基因座共有等位基因数的全同胞关系判别标准。方法根据280对全同胞及2003对无关个体Identifiler系统15个STR基因座的分型结果,对15个STR基因座的共有等位基因数（S15）和全同胞指数（FSI）进行统计,应用SAS8.2软件包得出Fisher判别函数并与ITO法结果进行比较。结果全同胞对及无关个体对中共有等位基因数目均符合正态分布。采用Identifiler系统15个STR基因座共有等位基因数进行全同胞关系判别时,判别函数分别为：ZFS=3.26970S15-31.51174和ZUI=1.70058S15-8.52411。用上述判别函数进行全同胞/无关个体关系判别时的平均错判率为0.0298。15个STR基因座共有等位基因数法、CODIS13个STR基因座共有等位基因数法与ITO法判别结果差异无统计学意义。结论应用常染色体STR基因座的共有等位基因数判别全同胞关系简便、可信,易于掌握且不受STR基因座等位基因频率的影响。