Genetic variation analysis of 15 autosomal STR loci of AmpFℓSTR® Sinofiler™ PCR Amplification Kit in Henan (central China) Han population

Developmental validation of the ANDE™ rapid DNA system with FlexPlex™ assay for arrestee and reference buccal swab processing and database searching

A developmental validation was performed to demonstrate reliability, reproducibility and robustness of the ANDE System with the FlexPlex assay, including an integrated Expert System, across a number of laboratories and buccal sample variations. Previously, the related DNAscan™/ANDE 4C Rapid DNA System using the PowerPlex^®16 assay and integrated Expert System Software received NDIS approval in March 2016. The enhanced ANDE instrument, referred to as ANDE 6C, and the accompanying 6-dye, 27-locus STR assay, referred to as FlexPlex, have been developed to be compatible with all widely used global loci, including the expanded set of the CODIS core 20 loci. Six forensic and research laboratories participated in the FlexPlex Rapid DNA developmental validation experiments, testing a total of 2045 swabs, including those obtained from 1387 unique individuals. The goal of this extensive and comprehensive validation was to thoroughly evaluate and document the ANDE System and its internal Expert System to reliably genotype reference buccal swab samples in a manner compliant with the FBI's Quality Assurance Standards and the NDIS Operational Procedures. The ANDE System, including automated Expert System analysis, generated reproducible and concordant results for buccal swabs when testing various instruments at different laboratories by a number of different operators. When testing a number of non-human DNAs, including oral bacteria, the ANDE System and FlexPlex assay demonstrated limited cross-reactivity. Potential PCR inhibitors were evaluated as part of the validation and no inhibition was detected. Reproducible and concordant profiles were generated from buccal swab samples collected with a limit of detection appropriate for buccal swab collections from arrestees. The precision and resolution of the System met industry standards for detection of microvariants and single base resolution. The integrated Expert System appropriately demonstrated the ability to correctly pass or fail profiles for CODIS upload without human review. During this comprehensive developmental validation, the ANDE System successfully interpreted over 2000 samples tested with over 99.99% concordant alleles. The data package described herein led to the ANDE System with the FlexPlex assay receiving NDIS approval in June 2018.

Forensic investigation of 23 autosomal STRs and application in Han and Mongolia ethnic groups

A forensic validation study of the Early Access Huaxia™ Platinum Polymerase Chain Reaction (PCR) kit was completed to document the performance capabilities and limitations. The genotyping of DNA samples was consistent across a large range of template DNA concentrations, with complete profiles obtained at 0.125 ng; however, no more than 2 mm × 1.2 mm punches of samples would be recommended for direct amplification. The size precision and accuracy test revealed the genotyping ability; while consistent results were obtained when comparing the kit with other commercially available systems. In addition, the whole PCR amplification can finish within approximately 45 min, making the system suitable for fast-detection. However, only partial profiles may be obtained with challenging samples, including DNA stored on Foam-Tipped Applicators (FTA) cards or some case samples. For the forensic application in ethnic groups, a total of 282 and 229 alleles were obtained in Han and Mongolia, respectively. Since the 23 short tandem repeats were independent from each other, the cumulative power of exclusion in duos was 0.999 999 157 188 and the cumulative power of exclusion in trios was 0.999 999 999 859 in the Han group while the cumulative power of exclusion in duos (CPE_duo) was 0.999 998 848 26 and cumulative power of exclusion in trios (CPE_trio) was 0.999 999 999 79 in the Mongolia group. And good internal consistency was found between the two investigated groups and the Sichuan Han, Hui, Tibetan and Uygur according to available reference data.

The allele combinations of three loci based on, liver, stomach cancers, hematencephalon, COPD and normal population: A preliminary study

The purpose of this study was to examine the specific allele combinations of three loci connected with the liver cancers, stomach cancers, hematencephalon and patients with chronic obstructive pulmonary disease (COPD) and to explore the feasibility of the research methods. We explored different mathematical methods for statistical analyses to assess the association between the genotype and phenotype. At the same time we still analyses the statistical results of allele combinations of three loci by difference value method and ratio method. All the DNA blood samples were collected from patients with 50 liver cancers, 75 stomach cancers, 50 hematencephalon, 72 COPD and 200 normal populations. All the samples were from Chinese. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler plus PCR amplification kit (15 STR loci). Previous research was based on combinations of single-locus alleles, and combinations of cross-loci (two loci) alleles. Allele combinations of three loci were obtained by computer counting and stronger genetic signal was obtained. The methods of allele combinations of three loci can help to identify the statistically significant differences of allele combinations between liver cancers, stomach cancers, patients with hematencephalon, COPD and the normal population. The probability of illness followed different rules and had apparent specificity. This method can be extended to other diseases and provide reference for early clinical diagnosis.

Screening of intracerebral hemorrhage associated allele combinations at different loci using a novel association analysis

BACKGROUND

Genetic research has progressed along with scientific and technological developments. However, it is difficult to identify frequency differences in the allele combination at cross-loci.

OBJECTIVE

The purpose of this study was to examine the relationship between the presence of specific allele combinations of short tandem repeat (STR) loci and the onset of intracerebral hemorrhage (ICH) using a novel methodology.

METHODS

DNA samples were collected from patients with ICH, who were adult population. There were a total of 51 Chinese patients (102 chromosomes), comprising 30 males and 21 females. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler Plus PCR amplification kit (15 STR loci). Statistically significant differences between observed and expected frequencies of allele combinations were identified. To further determine allele combinations related to the disease, analyses of patient age at disease onset for those carrying a specific allele combination were conducted. Finally, cross-validation of the two sets of analytical results was carried out.

RESULTS

A total of 1550 pairwise combinations were obtained by computer counting, of which eight pairs of alleles showed significant differences between the observed and expected frequencies (p<0.05, from 0.006 to 0.042). The p value for the cross-validation analysis was less than 0.05 for two pairs of alleles (D13S317-11 and vWA-17, p=0.021; D7S820-13 and D2S1338-18, p=0.023).

CONCLUSIONS

The study identified each population had a unique gene distribution and that distribution followed certain rules. ICH onset may be associated with this allele combinations (D13S317-11 and vWA-17; D7S820-13 and D2S1338-18). The new methodology used in this study could enable additional discoveries pertaining to the relationship between specific allele combinations at different loci and the onset of complex diseases.

Distributions of allele combination in single and cross loci among patients with several kinds of chronic diseases and the normal population

Genetic research has progressed along with scientific and technological developments. However, it is difficult to identify frequency differences in a particular allele distribution at a single locus. Such differences can be identified by examining the allele combination distribution. We explored different mathematical methods for statistical analyses to assess the association between the genotype and phenotype. We investigated the frequency distributions of alleles, combinations of single-locus genes, and combinations of cross-loci genes at 15 loci using 447 blood samples of 200 normal subjects, 72 patients with chronic obstructive pulmonary resistance, 50 liver cancers, 75 stomach cancers and 50 hematencephalon and identified each population as having a unique gene distribution and that the distribution followed certain rules. The probability of illness followed different rules and had apparent specificity. Differences obtained using statistics of combinations of cross-loci genes are superior to single-locus gene statistics, and combinations of single-locus gene statistics are better than allelic statistics.

Screening of longevity-associated genes based on a comparison between dead and surviving populations

AIM

To investigate longevity-associated genes based on a comparison between dead and surviving populations.

METHODS

A total of 71 cases of dead individuals were treated as the death group, and healthy volunteers who were matched with the dead individuals based on sex and age were recruited as the survival group. Alleles of 13 CODIS STR loci were determined using the AmpFLSTR Profiler Plus PCR Amplification Kit. The cross-validation was performed based on differences between the two groups in both frequency values and ages.

RESULTS

The frequency value of the D18S51-17 alleles was significantly higher in the dead group than in the survival group (p<0.05), and the frequency value of the D2S1338-18 allele was statistically lower in the dead group than in the survival group (p<0.05). The mean age of the subjects with the D2S1338-18 allele was also significantly higher than that of the subjects without D2S1338-18, and no significant difference was observed with respect to the other three alleles.

CONCLUSIONS

The results suggest that D2S1338-18 is associated with longevity.

Characterising the STR locus D6S1043 and examination of its effect on stutter rates

The forensic analysis of DNA is most often undertaken by the amplification of short tandem repeats (STR) using the polymerase chain reaction (PCR). DNA amplification can result in production of the target allele amplicon and a by-product called stutter. Stutter is the result of the miscopy of the target allele and is typically one repeat smaller. Stutter is traditionally described as a ratio of stutter and allele height; stutter ratio (SR). The challenge to DNA profile interpretation is most serious whenever stutter products are of a similar height to the minor allelic peaks in a mixed DNA profile. An accurate assignment of peaks and the prediction of their height is important when objectively interpreting forensic DNA profiles. The longest uninterrupted stretch (LUS) of tandem repeats within the allele has previously been shown to be a good predictor of stutter ratio. LUS is determined by sequencing a range of observed alleles at a locus. The locus D6S1043 is a relatively new locus to appear in commercial forensic DNA testing kits. To date however, there has been no comprehensive report of sequencing of this locus. In this work, we sequence a sample of D6S1043 alleles to determine LUS values and investigate allele repeat number and LUS as explanatory variables for SR.

Fully integrated, fully automated generation of short tandem repeat profiles

Background

The generation of short tandem repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short tandem repeat profiles from buccal swab samples, to improve forensic laboratory process flow as well as to enable short tandem repeat profile generation to be performed in police stations and in field-forward military, intelligence, and homeland security settings.

Results

An integrated system was developed consisting of an injection-molded microfluidic BioChipSet cassette, a ruggedized instrument, and expert system software. For each of five buccal swabs, the system purifies DNA using guanidinium-based lysis and silica binding, amplifies 15 short tandem repeat loci and the amelogenin locus, electrophoretically separates the resulting amplicons, and generates a profile. No operator processing of the samples is required, and the time from swab insertion to profile generation is 84 minutes. All required reagents are contained within the BioChipSet cassette; these consist of a lyophilized polymerase chain reaction mix and liquids for purification and electrophoretic separation.

Profiles obtained from fully automated runs demonstrate that the integrated system generates concordant short tandem repeat profiles. The system exhibits single-base resolution from 100 to greater than 500 bases, with inter-run precision with a standard deviation of ±0.05 - 0.10 bases for most alleles. The reagents are stable for at least 6 months at 22°C, and the instrument has been designed and tested to Military Standard 810F for shock and vibration ruggedization. A nontechnical user can operate the system within or outside the laboratory.

Conclusions

The integrated system represents the first generation of a turnkey approach to short tandem repeat profiling and has the potential for use in both the field (for example, police booking stations, the battlefield, borders and ports) and the forensic laboratory.

A 27-locus STR assay to meet all United States and European law enforcement agency standards

Different national and international agencies have selected specific STR sets for forensic database use. To enhance database comparison across national and international borders, a 27-locus multiplex system was developed comprising all 15 STR loci of the European standard set, the current 13 STR loci of the CODIS core, the proposed 22 STR loci of the expanded CODIS core, 4 additional commonly used STR loci, and the amelogenin locus. Development required iterative primer design to resolve primer-related artifacts, amplicon sizing, and locus-to-locus balance issues. The 19.5-min assay incorporated newly developed six-dye chemistry analyzed using a novel microfluidic electrophoresis instrument capable of simultaneous detection and discrimination of 8 or more fluorescent dyes. The 27-locus multiplex offers the potential for a new international STR standard permitting laboratories in any jurisdiction to use a single reaction to determine profiles for loci they typically generate plus an expanded common STR profiling set of global interest.

Complete paternal uniparental isodisomy for Chromosome 2 revealed in a parentage testing case

BACKGROUND

Uniparental disomy (UPD) is a rare cytogenetic event that has previously been reported mostly via genetic analysis of patients with phenotypes of recessive diseases. The incidence of UPD of any chromosome is estimated to be approximately1:3500 live births.

CASE REPORT

In a case of disputed paternity involving a phenotypically normal male child, mother-child exclusions were observed at five short tandem repeat markers, which were all located on Chromosome 2. Ten additional dinucleotide repeat markers spanning both arms of Chromosome 2 were investigated. The results revealed that the child was homozygous for all markers tested with all alleles originating from a single paternal Chromosome 2, which was consistent with paternal UPD for Chromosome 2.

CONCLUSION

This case and other previous reports demonstrate that UPD poses a high risk for false exclusion and incorrect expert opinion. Furthermore, this case highlights that a conclusion of exclusion of paternity or maternity should not be postulated if multiple genetic incompatibilities are located on the same chromosome because of the occurrence of UPD.

The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data

Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses.