OBJECTIVES: To calculate genetic parameters of SNP loci in next generation sequencing kits, and to compare them with STR loci for establishing the conversion ratio between SNP and STR system effectiveness. METHODS: Hardy-Weinberg equilibrium tests were performed in 101 SNP loci of next generation sequencing kits （ForenSeq™ DNA Signature Prep kit and Precision ID Identity Panel kit）. The parameters of system effectiveness of SNP loci in the cases of personal identification, trios, duos, and alleged parents were calculated, which were compared with the genetic parameters of STR loci. RESULTS: Except 2 loci without the data of genotype frequency, other 99 SNP loci conformed to Hardy-Weinberg equilibrium tests （P>0.05）. In ForenSeq™ DNA Signature Prep kit, the CDP of 94 SNP loci was 1-1.152 1×10⁻³⁴, CPE_trio was 1-4.416 9×10⁻⁸, CPE_duo was 1-8.483 7×10⁻⁵, and CPE_AP was 1-1.222 7×10⁻¹². In Precision ID Identity kit, the CDP was 1-2.052 4×10⁻³³, CPE_trio was 1-8.709 3×10⁻⁸, CPE_duo was 1-1.163 8×10⁻⁴, and CPE_AP was 1-3.725 7×10⁻¹². In the cases of personal identification, trios, duos and alleged parents, the system effectiveness of 2.85, 4.51, 4.88 and 4.55 SNP loci was equal to that of 1 STR locus, respectively. CONCLUSIONS With high system effectiveness of SNP loci, the next generation sequencing kits is suitable for personal identification and paternity testing in forensic science.
DNA Fingerprinting ; Forensic Genetics/methods* ; Gene Frequency ; Genetics, Population ; Genotype ; High-Throughput Nucleotide Sequencing/instrumentation* ; Humans ; Microsatellite Repeats ; Paternity ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Reagent Kits, Diagnostic

OBJECTIVETo identify pathogenic mutations in a Chinese pedigree affected with methylmalonic academia for genetic counseling and prenatal diagnosis.

METHODSMolecular analysis of the MUT, MMACHC, MMAA and MMAB genes was performed for the proband with methylmalonic academia by Ion Torrent semiconductor sequencing. Candidate mutations were validated by Sanger sequencing. The couple was offered prenatal diagnosis via analyzing of the fetal DNA through amniocentesis.

RESULTSThe proband was found to be compound heterozygous for c.609G>A (p.Trp203X) and c.658-660del AAG (p.Lys220del) mutations, which were inherited respectively from each of his parents. Prenatal diagnosis showed that the fetus has inherited two wild-type parental alleles.

CONCLUSIONThe targeted Ion Torrent PGM sequencing has detected pathogenic mutations in the Chinese pedigree affected with methylmalonic academia, which has provided molecular evidence for clinical diagnosis, genetic counseling and prenatal diagnosis for the family.

Adult ; Alkyl and Aryl Transferases ; genetics ; Amino Acid Metabolism, Inborn Errors ; embryology ; genetics ; Asian Continental Ancestry Group ; genetics ; Base Sequence ; Carrier Proteins ; genetics ; China ; Female ; High-Throughput Nucleotide Sequencing ; instrumentation ; methods ; Humans ; Infant ; Male ; Methylmalonyl-CoA Mutase ; genetics ; Mitochondrial Membrane Transport Proteins ; genetics ; Molecular Sequence Data ; Mutation ; Pedigree ; Pregnancy ; Prenatal Diagnosis ; instrumentation ; methods

As one of the key technologies in biomedical research, DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years. This is largely due to the advent of newer generations of sequencing platforms, offering ever-faster and cheaper ways to analyze sequences. In our previous review, we looked into technical characteristics of the next-generation sequencers and provided prospective insights into their future development. In this article, we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications.
Animals ; DNA-Binding Proteins ; chemistry ; Epigenomics ; Gene Expression Profiling ; Genomics ; High-Throughput Nucleotide Sequencing ; instrumentation ; methods ; trends ; Humans ; Nanostructures ; RNA, Small Untranslated ; chemistry