OBJECTIVE: To carry out optical genome mapping (OGM) for a Chinese pedigree with a rare paracentric reverse insertion of chromosome 17. METHODS: A high-risk pregnant woman identified at the Prenatal Diagnosis Center of Hangzhou Women's Hospital in October 2021 and her family members were selected as the study subjects. Chromosome G banding analysis, fluorescence in situ hybridization (FISH), single nucleotide polymorphism array (SNP array) and OGM were applied to verify the balanced structural abnormality of chromosome 17 in the pedigree. RESULTS: Chromosomal karyotyping analysis and SNP array assay have identified a duplication of 17q23q25 in the fetus. Karyotyping analysis of the pregnant woman showed that the structure of chromosome 17 was abnormal, whilst SNP array has detected no abnormality. OGM revealed that the woman has carried a paracentric reverse insertion, which was confirmed by FISH. The karyotype of her husband was normal. CONCLUSION The duplication of 17q23q25 in the fetus has derived from a paracentric reverse insertion of chromosome 17 in its mother. OGM has the advantage for delineating balanced chromosome structural abnormalities.
Pregnancy ; Humans ; Female ; Pedigree ; In Situ Hybridization, Fluorescence ; Chromosomes, Human, Pair 17/genetics* ; East Asian People ; Chromosome Aberrations ; Prenatal Diagnosis ; Chromosome Mapping ; Chromosome Inversion

To investigate the efficacy and value of optical genome mapping (OGM) in detecting chromosomal structural variations. In a clinical study about high-precision analysis of genomic structural variation for complex genetic diseases, a retrospective study was performed on the cases with karyotyping at the department of Obstetrics and Gynecology, and Endocrinology of Peking Union Medical College Hospital from January to December 2021. Ten cases with abnormal karyotype was detected by OGM. Partial cases were verified by fluorescence in situ hybridization (FISH), SNP array or CNV-seq. Results of ten cases, nine were detected with abnormality by OGM, including unbalanced chromosomal rearrangements (n=3), translocation (n=5) and paracentric inversion (n=1), and the results were in concordance with other standard assays. However, one case with breakpoint and reconnected at centromere has not been detected. In conclusion, ten samples were comprehensively analyzed by karyotyping, FISH, SNP array or CNV-seq, and OGM, and results demonstrated that optical genome mapping as a new technology can not only detect unbalanced rearrangements such as copy number variants as well as balanced translocations and inversions, but more importantly, it can refine breakpoints and orientation of duplicated segments or insertions. So it can contribute to the diagnosis of genetic diseases and prevent birth defect. However, the current technology is not yet capable of detecting breakpoints of balanced structural variations lying within unmapped regions.
Chromosome Mapping ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Pregnancy ; Retrospective Studies ; Translocation, Genetic

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-specific expression data to narrow down the list of candidate genes/mutations and identified deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identified in mutant 531, which occurs within a ∼200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4 (RdDM4) and AMP-binding protein, respectively. This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies.
Chromosome Mapping ; methods ; DNA, Plant ; genetics ; DNA-Binding Proteins ; genetics ; Endosperm ; Exome ; genetics ; Exons ; genetics ; Gene Deletion ; Genomics ; Phenotype ; Plant Proteins ; genetics ; Sequence Analysis, DNA ; methods ; Transcription Factors ; genetics ; Zea mays ; genetics

We propose that locations of genes on chromosomes can contribute to the prediction of gene regulatory relationships. We constructed a time-based gene regulatory network of zebrafish cardiogenesis on the basis of a spatio-temporal neighborhood method. Through the network, specific regulatory pathways and order of gene expression during zebrafish cardiogenesis were obtained. By comparing the order with locations of these genes on chromosomes, we discovered that there exists a reversal phenomenon between the order and order of gene locations. The discovery provides an inherent rule to instruct exploration of gene regulatory relationships. Specifically, the discovery can help to predict if regulatory relationships between genes exist and contribute to evaluating the correctness of discovered gene regulatory relationships.
Algorithms ; Animals ; Chromosome Mapping ; Chromosomes ; Gene Expression ; Gene Regulatory Networks ; Heart/physiology* ; Zebrafish/genetics*

OBJECTIVE: To establish a 15-plex rapid STR multiplex amplification system. METHODS: Fourteen auto-chromosome loci and one sex-chromosome were selected to compare the situations of allelic losses and nonspecific amplication under different conditions. FastStart Taq DNA polymerase and DNA standard sample 9947A were used during amplification and optimization process.15-plex rapid STR amplification system was achieved by performing various experiments including selection of amplification conditions and the volume of DNA polymerase, adjustment of inter-locus balance, optimization of rapid amplification, screening of reaction buffers, selection of reaction volume, and a variety of additives. RESULTS: Using 10 μL rapid PCR system, including 1 ng DNA templates, 0.4 μL polymerase and 10xFastStart high fidelity reaction buffer, a complete and well-balance DNA profile of 15 STR loci for standard genomic DNA was obtained in 32 minutes, without the allele drop-out and non-specific amplicons. Meanwhile, 5% glycerinum, 0.01% gelatin, 0.05% gelatin and 5 mmol/L ammonium sulfate could be used as the reactive additive during the amplification procedure. CONCLUSION The 15-plex rapid STR multiplex amplification system can be used to decrease reaction time and enhance sample throughput.
Alleles ; Chromosome Mapping ; DNA/genetics* ; DNA Fingerprinting/methods* ; Forensic Genetics/methods* ; Humans ; Microsatellite Repeats/genetics* ; Polymerase Chain Reaction/methods* ; Racial Groups/genetics* ; Sensitivity and Specificity ; Tandem Repeat Sequences

Genetic polymorphisms within immunity-related candidate genes in pigs have been identified to control variations in immune functions and/or disease resistance. It has become necessary to evaluate the effects of other genetic markers of economically important traits prior to introducing them into marker-assisted selection programs. In this study, polymorphisms of porcine genes coding Interferon-induced Gunylate binding protein 1 (GBP1), GBP2, CD163, and CD169 were investigated for their association with growth and meat quality traits in a Korean native pig breed-Yorkshire inter-crossed F2 pig population (KY-F2). KY-F2 animals (n=346) have been successfully used for linkage mapping to identify quantitative loci that control meat quality, growth, and immunity traits. In our results, polymorphisms in genes GBP1 and GBP2 showed association with pig growth rate as well as meat quality traits such as crude fat, drip loss, and meat color (yellowness) in the KY-F2 population. The polymorphism in gene CD163 only showed association with crude fat, as a meat quality trait. CD169 gene was associated with pork tenderness. In conclusion, four immune-related genetic markers were validated for their association with growth and meat quality traits to gauge their potential use in a swine selection program. The results warrant further studies in other commercial pig populations.
Animals ; Carrier Proteins ; Chromosome Mapping ; Clinical Coding ; Disease Resistance ; DNA* ; Genetic Markers ; Meat* ; Polymorphism, Genetic ; Swine

Non-coding expansion spinocerebellar ataxias (SCAs) are a group of autosomal dominant neurodegenerative diseases characterized by "CTA/CTG", "ATTCT", "TGGAA" expansion in non-coding region of the causative gene. Until now, 5 subtypes including SCA8, SCA10, SCA12, SCA31 and SCA36 have been mapped. Recently, the causative mutation for SCA36, namely intronic hexanucleotide GGCCTG expansion in NOP56 gene, has been identified in Japanese and Spanish pedigrees in succession. Compared with other subtypes of SCAs, there are certain distinctive characteristics for SCA36. The clinical and genetic features of SCA36 are reviewed in this paper.
Base Sequence ; Biomedical Research ; methods ; trends ; Chromosome Mapping ; Chromosomes, Human, Pair 20 ; genetics ; DNA Repeat Expansion ; genetics ; Genetic Predisposition to Disease ; genetics ; Humans ; Nuclear Proteins ; genetics ; Oligonucleotides ; genetics ; Spinocerebellar Ataxias ; genetics ; pathology

The first genetic linkage map of Salvia miltiorrhiza was constructed in 94 F1 individuals from an intraspecific cross by using simple sequence repeat (SSR), sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. A total of 93 marker loci in the linkage map, consisting of 53 SSR, 38 SRAP and 2 ISSR locus were made up of eight linkage groups, covered a total length of 400.1 cm with an average distance of 4.3 cm per marker. The length of linkage groups varied from 3.3 -132 cm and each of them included 2-23 markers, separately. The result will provide important basis for QTL mapping, map-based cloning and association studies for commercially important traits in S. miltiorrhiza.
Chromosome Mapping ; Genetic Linkage ; Genetic Markers ; Microsatellite Repeats ; Polymorphism, Genetic ; Salvia miltiorrhiza ; genetics

Potocki-Shaffer syndrome (PSS, OMIM #601224) is a rare contiguous gene deletion syndrome caused by haploinsufficiency of genes located on the 11p11.2p12. Affected individuals have a number of characteristic features including multiple exostoses, biparietal foramina, abnormalities of genitourinary system, hypotonia, developmental delay, and intellectual disability. We report here on the first Korean case of an 8-yr-old boy with PSS diagnosed by high resolution microarray. Initial evaluation was done at age 6 months because of a history of developmental delay, hypotonia, and dysmorphic face. Coronal craniosynostosis and enlarged parietal foramina were found on skull radiographs. At age 6 yr, he had severe global developmental delay. Multiple exostoses of long bones were detected during a radiological check-up. Based on the clinical and radiological features, PSS was highly suspected. Subsequently, chromosomal microarray analysis identified an 8.6 Mb deletion at 11p11.2 [arr 11p12p11.2 (Chr11:39,204,770-47,791,278)x1]. The patient continued rehabilitation therapy for profound developmental delay. The progression of multiple exostosis has being monitored. This case confirms and extends data on the genetic basis of PSS. In clinical and radiologic aspect, a patient with multiple exostoses accompanying with syndromic features, including craniofacial abnormalities and mental retardation, the diagnosis of PSS should be considered.
Child ; Chromosome Deletion ; Chromosome Disorders/diagnosis/*genetics/radiography ; Chromosome Mapping ; Chromosomes, Human, Pair 11/genetics/radiography ; Craniofacial Abnormalities/genetics ; Developmental Disabilities/genetics ; Exostoses, Multiple Hereditary/diagnosis/*genetics/radiography ; Humans ; Male ; Muscle Hypotonia/genetics ; Oligonucleotide Array Sequence Analysis ; Rare Diseases/*genetics ; Republic of Korea

Potocki-Shaffer syndrome (PSS, OMIM #601224) is a rare contiguous gene deletion syndrome caused by haploinsufficiency of genes located on the 11p11.2p12. Affected individuals have a number of characteristic features including multiple exostoses, biparietal foramina, abnormalities of genitourinary system, hypotonia, developmental delay, and intellectual disability. We report here on the first Korean case of an 8-yr-old boy with PSS diagnosed by high resolution microarray. Initial evaluation was done at age 6 months because of a history of developmental delay, hypotonia, and dysmorphic face. Coronal craniosynostosis and enlarged parietal foramina were found on skull radiographs. At age 6 yr, he had severe global developmental delay. Multiple exostoses of long bones were detected during a radiological check-up. Based on the clinical and radiological features, PSS was highly suspected. Subsequently, chromosomal microarray analysis identified an 8.6 Mb deletion at 11p11.2 [arr 11p12p11.2 (Chr11:39,204,770-47,791,278)x1]. The patient continued rehabilitation therapy for profound developmental delay. The progression of multiple exostosis has being monitored. This case confirms and extends data on the genetic basis of PSS. In clinical and radiologic aspect, a patient with multiple exostoses accompanying with syndromic features, including craniofacial abnormalities and mental retardation, the diagnosis of PSS should be considered.
Child ; Chromosome Deletion ; Chromosome Disorders/diagnosis/*genetics/radiography ; Chromosome Mapping ; Chromosomes, Human, Pair 11/genetics/radiography ; Craniofacial Abnormalities/genetics ; Developmental Disabilities/genetics ; Exostoses, Multiple Hereditary/diagnosis/*genetics/radiography ; Humans ; Male ; Muscle Hypotonia/genetics ; Oligonucleotide Array Sequence Analysis ; Rare Diseases/*genetics ; Republic of Korea