Donor cell chimerism evaluation in cerebrospinal fluid by short tandem repeat analysis following allogeneic hematopoietic stem cell transplantation

Cerebrospinal fluid (CSF) cell count, morphology and flow cytometric evaluations are used to investigate central nervous system (CNS) involvement in leukemia/lymphoma. We performed CSF short tandem repeat (STR) analysis to monitor CSF chimerism status and evaluate for disease involvement in 11 asymptomatic pediatric allogeneic hematopoietic stem cell transplantation (HSCT) recipients with hemato-lymphoid neoplasms and high risk for or history of CNS involvement. Eighteen (64%) of the samples with median CSF cell count of 1/mm³ with 90% lymphocytes gave conclusive STR results, suggesting that this DNA-based method can be used in monitoring CSF chimerism status after HSCT with an acceptable yield.     

Performance characteristics of chimerism testing by next generation sequencing

Chimerism testing provides informative clinical data regarding the status of a biological sample mixture. For years, this testing was achieved by measuring the peaks of informative short tandem repeat (STR) loci using capillary electrophoresis (CE). With the advent of next generation sequencing (NGS) technology, the quantification of the percentage of donor/recipient mixtures is more easily done using sequence reads in large batches of samples run on a single flow cell. In this study, we present data on using a FORENSIC NGS chimerism platform to accurately measure the percentage of donor/recipient mixtures. We were able to detect chimerism to a limit threshold of 1% using both STR and single nucleotide polymorphism (SNP) informative loci. Importantly, a significant correlation was observed between NGS and CE chimerism methods when compared at donor detection ranges from 1% to 10%. Furthermore, 100% accuracy was achieved through proficiency testing over six surveys. Its usefulness was expanded beyond this to help identify suitable donors for solid organ transplant patients using ancestry SNP profiles. In summary, the NGS method provides a sensitive and reliable alternative to traditional CE for chimerism testing of clinical samples.     

Correlation Analyses Reveal a Substantial Influence of Allelic Gaps on the Investigation of Genetic Diversity of Modern Human Populations with Microsatellites

High intra-population genetic diversity and multiple measures of genetic variability at STR loci are useful in inferring past evolutionary history. However, STRs, categorized by their repeat motif size, differ in a number of aspects, requiring separate analyses. We analyzed 783 STRs in 36 worldwide populations to examine marker suitability as well as correlations between various measurements, to evaluate the extent of genomic diversity present in modern human populations. The loci were grouped by type and analyzed separately for each population group. Genetic variation defined by gene diversity and allele size variance, shows different trends of variation across four types of STRs. Additionally, there is little variation of genetic diversity, but there is decreased allelic size variance with increasing repeat motifs. A poor correlation between genetic diversity and allelic size variance across loci in all groups for Di-STRs is probably caused by the presence of allelic size gaps. In contrast, allelic size variance, genetic diversity, and number of alleles are strongly correlated with both tri- and tetra-STRs. The positive correlation of allelic size variance and presence of gaps within the range of allelic sizes in Di-STRs alone explains these observations. An unexpected high imbalance index (β) at Di-STRs due to high allelic size variance also supports this assertion.     

Investigation of the dopamine D5 receptor gene (DRD5) in adult attention deficit hyperactivity disorder

Several lines of evidence from neuroimaging, pharmacology and genetics support the involvement of the dopaminergic system in the etiology of Attention Deficit Hyperactivity Disorder (ADHD). Previous candidate gene studies have investigated the association between a dinucleotide (CA)_n repeat polymorphism, located 18.5 kb from the start codon of the DRD5 gene, and ADHD. Association between the 148 bp allele and ADHD has been reported in some studies, however replication of the finding has not been consistent. We tested for an association between the (CA)_n repeat and adult ADHD in a sample comprised of 119 families with adult ADHD probands and 88 unrelated adult ADHD cases with a corresponding number of controls matched for age, ethnicity and sex. In the family sample we found a non-significant trend for association between the 148 bp allele and ADHD (Z = 1.91, p = 0.055). An excess of non-transmissions was detected for the 150 and 152 bp alleles (Z = −2.26, p = 0.023; Z = −2.20, p = 0.028). Quantitative analysis performed using the Brown Attention Deficit Disorder Scale (BADDS) showed association between the 150 bp allele and lower total score (p = 0.011), and lower effort (p = 0.008), activation (p = 0.008) and attention (p = 0.01) cluster scores. We did not replicate association findings in the case–control group, likely due to the lack of statistical power of this sample. Our findings add to the literature suggesting DRD5 (CA)_n repeat has a modest effect in modulating susceptibility to adult ADHD but further studies are required.     

South Indian men with reduced CAG repeat length in the androgen receptor gene have an increased risk of prostate cancer

The androgen receptor (AR) gene possesses polymorphic CAG tandem repeats and the repeat length has been inversely related to the risk of prostate cancer (PCa). The distinct ethnic variation in the CAG repeat length may be correlated to differences in PCa risk in different populations. To evaluate the CAG repeat length in the AR gene and the implications for PCa, we screened 87 PCa patients and 120 control subjects from South India. The mean CAG repeat length in PCa patients was significantly smaller than that of controls (17.0 vs 20.7; P<0.001). Men with 19 CAG repeats had a significantly increased risk of cancer compared to those with >19 CAG repeats (age-adjusted OR=7.01; 95% CI=3.52–13.94; P<0.001). However, no significant association was observed between CAG repeats and age of onset or prostate-specific antigen levels. Although there was a trend towards shorter CAG repeat length in high grades of cancer, it was not significant (P=0.085). Thus, our results suggest an association between short CAG repeats in the AR gene and PCa risk in South Indian men. Further, we propose that CAG repeats could be used as a prognostic marker for PCa diagnosis.     

15个STR基因座的种属特异性研究

目的研究15个STR基因座对常见9种动物的种属特异性，探讨其在法医学中的应用价值。方法对9种常见动物肌肉组织的DNA进行PCR扩增，ABI310遗传分析仪进行DNA分型，测定15个STR基因座的种属特异性。结果用15对SIR基因座引物分别对9种常见动物肌肉组织的DNA进行PCR扩增检测CSFIPO，B8S1179，D19S433基因座时，9种动物均有PCR扩增产物；检测1321S11，197S820，D13S317，D16S539，TPOX，D18S51，D5s818，FGA，D3S1358基因座时，部分动物有PCR扩增产物，其中TPOX，D21S11基因座扩增产物片段长度明显与人的不同。这9种动物在D2S1338、vWA、TH01基因座均没有扩增产物。结论在15个STR基因座中，3个基因座只对人DNA有扩增产物，有较好的种属特异性；9个基因座对人和部分动物均有扩增产物，但产物的片段大小与人不同，在进行个人识别时，可以用其分析DNA的种属来源；3个基因座对人和动物均有扩增产物，且片段长度相近，在进行个人识别时，应先作DNA种属来源检查。     

Power of exclusion revisited: probability of excluding relatives of the true father from paternity

In parentage testing using DNA markers, the formulae for calculating the probability of exclusion generally overstate the power of a test battery by considering its ability to exclude a random man. It is known that in many cases, in particular immigration applications, the false father is more likely to be a relative, e.g. brother, of the true father than an unrelated man. This work presents formulae that take this consideration into account. A practical example using Hong Kong data is provided to illustrate the effect of the modification. Also discussed is how the expected efficacy of a test battery will be affected when possible mutations and null alleles or genetic inconsistencies are taken into consideration. Received: 4 August 2000 / Accepted: 7 January 2001     

Trajectory reconstruction from trace evidence on spent bullets. II. Are tissue deposits eliminated by subsequent impacts?

STR-based individualisation of biological deposits on bullets after perforation of tissue, can identify the person injured or killed by a particular bullet and comparison with the firearms used can identify the weapon and thus possibly the person who did the shooting. In this study, the effect of subsequent impacts on intermediate targets such as loss of cells was investigated by amplification of mitochondrial (mt) DNA. Bovine tissue was perforated and the 9 mm Luger FMJ bullets were recovered from the bullet collector. The mt cytochrome-b (cyt-b) gene could be amplified by the polymerase chain reaction (PCR) from 14 out of 15 bullets. Examination with a scanning electron microscope (SEM) and an energy-dispersive X-ray spectrometer (EDS) demonstrated the presence of minute dried tissue deposits on all bullets (n = 10) but was not able to establish preferential locations. In a series of 25 gunshots, various intermediate targets (glass, wood, car metal, gypsum board, asphalt) were perforated/ impacted following perforation of tissue and the cyt-b gene could be typed from all bullets. It is concluded that subsequent impacts on intermediate targets do not eliminate enough biological deposits to render DNA analysis impossible and that the amplification of mtDNA is a useful additional method. Received: 5 September 2000 / Accepted: 25 November 2000     

DNA commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs

During the past few years the DNA commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area, namely Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods. Received: 19 April 2001     

Identification and characterization of two novel human polymorphic STRs on the Y chromosome

From sequence database information, we have identified two male-specific and polymorphic tetranucleotide STRs, DYS 441 (GDB:10013873) and DYS 442 (GDB: 10030304), on the Y chromosome. Analysis of 184 males allowed 7 and 5 alleles to be distinguished in the DYS 441 and DYS 442 systems, respectively, yielding 21 haplotypes. The gene diversities were 0.72 and 0.51, respectively and the haplotype diversity was 0.85. Received: 16 October 2000 / Accepted: 7 January 2001