Application Progress of Massively Parallel Sequencing Technology in STR Genetic Marker Detection / 法医学杂志

In recent years, more and more forensic genetics laboratories have begun to apply massively parallel sequencing (MPS) technology, that is, next-generation sequencing (NGS) technology, to detect common forensic genetic markers, including short tandem repeat (STR), single nucleotide polymorphism (SNP), the control region or whole genome of mitochondrial DNA (mtDNA), as well as messenger RNA (mRNA), etc., for forensic practice, such as individual identification, kinship analysis, ancestry inference and body fluid identification. As the most widely used genetic marker in forensic genetics, STR is currently mainly detected by capillary electrophoresis (CE) platform. Compared with CE platform, MPS technology has the advantages of simultaneous detection of a large number of genetic markers, massively parallel detection of samples, the polymorphism of sequence detected by NGS makes STR have the advantages of higher resolution and system efficiency. However, MPS technology is expensive, there is no uniform standard so far, and there are problems such as how to integrate MPS-STR data with the existing CE-STR database. This review summarizes the current status of the application of MPS technology in the detection of STR genetic markers in forensic genetics, puts forward the main problems that need to be solved urgently, and prospects the application prospect of this technology in forensic genetics.

Forensic Application of ForenSeqTM DNA Signature Prep Kit in Zhengjiang She Ethnic Group / 法医学杂志

OBJECTIVES@#To evaluate the ability of the ForenSeqTM DNA Signature Prep kit (ForenSeq kit) in analyzing the sequence information of STRs in Zhejiang She ethnic group and its forensic application efficacy.@*METHODS@#A total of 50 Zhejiang She ethnic group samples were sequenced with the ForenSeq kit on the MiSeq FGx platform. The data was analyzed using ForenSeqTM universal analysis software to obtain the motif structure and flank regions of the 58 STRs, then compared with PCR-CE typing results to test the consistency. At last, the allele frequency and population genetic parameters were calculated.@*RESULTS@#A total of 448 sequence polymorphic alleles were detected in 50 samples of Zhejiang She ethnic group. Compared with fragment length polymorphism detected by PCR-CE, 82 alleles were increased by MPS detection based on ForenSeq kit, and 7 SNPs variation were detected in the flanking regions of 6 loci. The 22 male individuals were genotyped, and total 19 haplotypes were detected in 24 Y chromosome STRs of these 22 males. The cumulative discrimination power of the 27 autosomal STRs was 1-8.87×10-30, the cumulative probability of exclusion of duo-testing was 0.999 999 962 640 657, the cumulative probability of exclusion of trios-testing was 0.999 999 999 999 633.@*CONCLUSIONS@#Based on MPS typing technology, using the ForenSeq kit greatly improves the detection efficiency. In addition, the 58 STRs have good genetic polymorphisms in Zhejiang She ethnic group, which are suitable for individual identification and paternity identification in forensic application.

Targeted massively parallel sequencing for congenital generalized lipodystrophy

ABSTRACT Objective: Our aim is to establish genetic diagnosis of congenital generalized lipodystrophy (CGL) using targeted massively parallel sequencing (MPS), also known as next-generation sequencing (NGS). Subjects and methods: Nine unrelated individuals with a clinical diagnosis of CGL were recruited. We used a customized panel to capture genes related to genetic lipodystrophies. DNA libraries were generated, sequenced using the Illumina MiSeq, and bioinformatics analysis was performed. Results: An accurate genetic diagnosis was stated for all nine patients. Four had pathogenic variants in AGPAT2 and three in BSCL2. Three large homozygous deletions in AGPAT2 were identified by copy-number variant analysis. Conclusions: Although we have found allelic variants in only 2 genes related to CGL, the panel was able to identify different variants including deletions that would have been missed by Sanger sequencing. We believe that MPS is a valuable tool for the genetic diagnosis of multi-genes related diseases, including CGL.

Osteogénesis imperfecta tipo IV originada en una rara variante de cambio de sentido en COL1A2 / Osteogenesis imperfecta type IV originated in a rare variant of change of direction in COL1A2

Resumen La osteogénesis imperfecta es una rara anomalía genética que se carac teriza por una baja masa ósea y susceptibilidad aumentada a fracturas. La mayoría de los casos se asocian a variantes en los genes COL1A1 y COL1A2 que codifican para el colágeno tipo I. Se ha clasificado en cua tro tipos, siendo el tipo IV el menos frecuente. Se presenta un caso de osteogénesis imperfecta tipo IV en una niña de seis meses, quien tenía escleras azules y acortamiento bilateral del fémur y desviación en varo de la tibia. Las radiografías mostraron desproporción craneofacial y hue sos wormianos, fusión atlanto-odontoidea; luxación coxo-femoral bila teral congénita, acortamiento y desviación del fémur bilateral, fractura antigua en fémur derecho y osteopenia generalizada. Se realizó panel molecular que incluyó los genes ALPL, COL1A1, COL1A2 e IFITM5, mos trando en COL1A2 una transición en heterocigosis de guanina a adenina (c.2531G>A), cambio asociado con osteogénesis imperfecta. El objetivo de este reporte es brindar información sobre la presentación clínica, los métodos diagnósticos y las posibilidades terapéuticas de una rara enfer medad genética.

Abstract Osteogenesis imperfecta is a rare genetic anomaly characterized by low bone mass and increased susceptibility to fractures. The majority of cases are associated with variants in the COL1A1 and COL1A2 genes that code for type I collagen. It has been classified into four types, with type IV being the least frequent. We present a case of osteogenesis imperfecta type IV in a six-month-old girl, who had blue scleras and bilateral shortening of the femur and varus deviation of the tibia. X-rays showed craniofacial disproportion and wormian bones, atlanto-odontoid fusion; bilateral congenital bilateral coxo-femoral dislocation, shortening and deviation of the bilateral femur, old fracture in the right femur and generalized osteopenia. A molecular panel was carried out that included the ALPL, COL1A1, COL1A2 and IFITM5 genes, showing in COL1A2 a transition in guanine to adenine heterozygosis (c.2531G>A), a change associated with osteogenesis imperfecta. The objective of this report is to provide information on the clinical presentation, diagnostic methods and therapeutic possibilities of a rare genetic disease.

Application Prospect of Massively Parallel Sequencing in Mixed Stain Detection / 法医学杂志

Mixed stains is the common biological sample in sexual crime cases. Its analysis and DNA profiles interpretation are one of the difficulties in forensic examination. The current genetic marking of mixed stain detection mainly rely on capillary electrophoresis （CE） separation technology, and the analysis methods of the results are mainly inclusion rate and likelihood methods. Because CE has limited resolution and is not able to exploit the efficacy of each genetic marker, its ability to split mixed stain is limited. In recent years, the emerging massively parallel sequencing （MPS） technique not only can obtain the base sequence information of genetic markers, but also is capable of detecting multiple genetic markers simultaneously, and thus derives new analytical methods, bringing new opportunities for forensic detection and analysis of mixed stain. This paper intends to review the application prospects of conventional mixed stain analyses and MPS technique, therefore to provide references for later research and practice.

Clinical Validation of Non-Invasive Prenatal Testing for Fetal Common Aneuploidies in 1,055 Korean Pregnant Women: a Single Center Experience

BACKGROUND: Non-invasive prenatal testing (NIPT) using cell-free fetal DNA from maternal plasma for fetal aneuploidy identification is expanding worldwide. The objective of this study was to evaluate the clinical utility of NIPT for the detection of trisomies 21, 18, and 13 of high-risk fetus in a large Korean population. METHODS: This study was performed retrospectively, using stored maternal plasma from 1,055 pregnant women with singleton pregnancies who underwent invasive prenatal diagnosis because of a high-risk indication for chromosomal abnormalities. The NIPT results were confirmed by karyotype analysis. RESULTS: Among 1,055 cases, 108 cases of fetal aneuploidy, including trisomy 21 (n = 57), trisomy 18 (n = 42), and trisomy 13 (n = 9), were identified by NIPT. In this study, NIPT showed 100% sensitivity and 99.9% specificity for trisomy 21, and 92.9% sensitivity and 100% specificity for trisomy 18, and 100% sensitivity and 99.9% specificity for trisomy 13. The overall positive predictive value (PPV) was 98.1%. PPVs for trisomies 21, 18, and 13 ranged from 90.0% to 100%. CONCLUSION: This study demonstrates that our NIPT technology is reliable and accurate when applied to maternal DNA samples collected from pregnant women. Further large prospective studies are needed to adequately assess the performance of NIPT.

Detection of Innate and Artificial Mitochondrial DNA Heteroplasmy by Massively Parallel Sequencing: Considerations for Analysis

BACKGROUND: Mitochondrial heteroplasmy, the co-existence of different mitochondrial polymorphisms within an individual, has various forensic and clinical implications. But there is still no guideline on the application of massively parallel sequencing (MPS) in heteroplasmy detection. We present here some critical issues that should be considered in heteroplasmy studies using MPS. METHODS: Among five samples with known innate heteroplasmies, two pairs of mixture were generated for artificial heteroplasmies with target minor allele frequencies (MAFs) ranging from 50% to 1%. Each sample was amplified by two-amplicon method and sequenced by Ion Torrent system. The outcomes of two different analysis tools, Torrent Suite Variant Caller (TVC) and mtDNA-Server (mDS), were compared. RESULTS: All the innate heteroplasmies were detected correctly by both analysis tools. Average MAFs of artificial heteroplasmies correlated well to the target values. The detection rates were almost 90% for high-level heteroplasmies, but decreased for low-level heteroplasmies. TVC generally showed lower detection rates than mDS, which seems to be due to their own computation algorithms which drop out some reference-dominant heteroplasmies. Meanwhile, mDS reported several unintended low-level heteroplasmies which were suggested as nuclear mitochondrial DNA sequences. The average coverage depth of each sample placed on the same chip showed considerable variation. The increase of coverage depth had no effect on the detection rates. CONCLUSION: In addition to the general accuracy of the MPS application on detecting heteroplasmy, our study indicates that the understanding of the nature of mitochondrial DNA and analysis algorithm would be crucial for appropriate interpretation of MPS results.

The application of non-invasive prenatal genetic sequencing for fetal chromosomal aneuploidy / 国际检验医学杂志

Objective To explore the efficiency and the clinical application value of non-invasive prenatal genetic testing for fetal chromosomal aneuploidy.Methods A total of 1 865 pregnant women treated in Guangdong Women and Children Hospital from January 201 1 to January 2013 were selected.Inclusion criteria:advanced age,prenatal screening for high risk,and fetal abnormality indicated by color ultrasonography,agreeing with non-invasive prenatal genetic testing.After non-invasive prenatal genetic testing, the pregnant women with positive result underwent cell culture and chromosomal karyotyping.Following the situations after deliv-ery were designed as the final criteria for definite diagnosis of fetal chromosomal aneuploidy.Results A total of 1 865 pregnant women underwent non-invasive prenatal genetic testing,of which 21 pregnant women were found with positive result,including 14 pregnant women with trisomy 21,5 pregnant women with trisomy 18,2 pregnant women with trisomy 13.The results of chromo-somal karyotyping after amniocentesis or umbilical cord blood puncture were designed as golden standard.Among the women with trisomy 21,one woman refused the prenatal diagnosis,self induced labor and could not be confirmed karyotype.No false positive case was found among the women with trisomy 18 and 13.No missed diagnosis was found among the pregnant women with negative result during follow-up after delivery.Through statistical analysis of non-invasive prenatal fetal genetic testing,the sensitivity for the trisomy 21 was 100%,and the accuracy was 92.9%.The sensitivity and accuracy for the trisomy 18 and 13 were 100%.Conclu-sion Non-invasive prenatal genetic testing can improve the diagnostic efficacy before delivery,reduce the birth of ill infants,and it is a quick,safe,easy-accepted and reliable prenatal diagnostic method,which is worthy to be popularized and an inexorable trend of development in the future.

Introduction to bioinformatics: sequencing technology

Bioinformatics, the study of integrating high throughput biological data and statistical model through intensive computation, has been attracting great interest in recent times and Sequencing is at the very center of it. The large amount of information obtained from sequencing has deepened our understanding and fundamental knowledge of organisms. This review will aim to provide a brief summary of new sequencing technology, current issues, and projects focused on medical applications. The article is organized in three parts. Part I explains common terminologies and background of sequencing technology, and Part II compares distinct features of currently available platforms. Part III contains applications in various medical fields.