RESUMEN
The need to identify a missing person (MP) through kinship analysis of DNA samples found at a crime scene has become increasingly prevalent. DNA samples from MPs can be severely degraded, contain little DNA and mixed with other contributors, which often makes it difficult to apply conventional methods in practice. This study developed a massively parallel sequencing-based panel that contains 1661 single-nucleotide polymorphisms (SNPs) with low minor allele frequencies (MAFs) (averaged at 0.0613) in the Chinese Han population, and the strategy for relationship inference from DNA mixtures comprising different numbers of contributors (NOCs) and of varying allele dropout probabilities. Based on the simulated dataset and genotyping results of 42 artificial DNA mixtures (NOC = 2-4), it was observed that the present SNP panel was sufficient for balanced mixtures when referenced to the closest relatives (parents/offspring and full siblings). When the mixture profiles suffered from dropout, incorrect assignments were markedly associated with relatedness, NOC and the dropout level. We, therefore, indicate that SNPs with low MAFs could be reliably interpreted for MP identification through the kinship analysis of complex DNA mixtures. Further studies should be extended to more possible scenarios to test the feasibility of this present approach.
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With the extensive application of highly sensitive genetic techniques in the field of prenatal diagnosis, prenatal chromosomal mosaicisms including true fetal mosaicisms and confined placental mosaicisms are frequently identified in clinical settings, and the diagnostic criteria and principle of genetic counseling and clinical management for such cases may vary significantly among healthcare centers across the country. This not only has brought challenges to laboratory technician, genetic counselor and fetal medicine doctor, but can also cause confusion and anxiety of the pregnant woman and their family members. In this regard, we have formulated a consensus over the prenatal diagnosis and genetic counseling for chromosomal mosaicisms with the aim to promote more accurate and rational evaluation for fetal chromosomal mosaicisms in prenatal clinics.
Asunto(s)
Asesoramiento Genético , Mosaicismo , Consenso , Femenino , Humanos , Placenta , Embarazo , Diagnóstico Prenatal/métodosRESUMEN
BACKGROUND: Hydatidiform moles exhibit a distinctive gross appearance of multiple vesicles in the placenta. The advances in cytogenetic technologies have helped uncover novel entities of hydatidiform moles and enabled elaborate diagnoses. However, management of a vesicular placenta with a coexistent live fetus poses a bigger challenge beyond hydatidiform moles. CASE PRESENTATION: A 33-year-old woman was referred to our department for suspected hydatidiform mole coexistent with a live fetus at 24 weeks' gestation. The patient had conceived through double embryo transplantation, and first-trimester ultrasonography displayed a single sac. Mid-trimester imaging findings of normal placenta parenchyma admixed with multiple vesicles and a single amniotic cavity with a fetus led to suspicion of a singleton partial molar pregnancy. After confirmation of a normal diploid by amniocentesis and close surveillance, the patient delivered a healthy neonate. Preliminary microscopic examination of the placenta failed to clarify the diagnosis until fluorescence in situ hybridization showed a majority of XXY sex chromosomes. The patient developed suspected choriocarcinoma and achieved remission for 5 months after chemotherapy, but relapsed with suspected intermediate trophoblastic tumor. CONCLUSION: We report a rare case of twin pregnancy comprising a partial mole and a normal fetus that resembled a singleton partial molar pregnancy. Individualized care is important in conditions where a vesicular placenta coexists with a fetus. We strongly recommend ancillary examinations in addition to traditional morphologic assessment in such cases.
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Mola Hidatiforme/diagnóstico , Placenta/patología , Embarazo Gemelar , Neoplasias Uterinas/diagnóstico , Adulto , Femenino , Feto , Edad Gestacional , Humanos , Hibridación Fluorescente in Situ , Nacimiento Vivo , Embarazo , Primer Trimestre del Embarazo , Ultrasonografía PrenatalRESUMEN
Hb A2 levels are usually high in carriers of ß-thalassemia (ß-thal). These levels also provide a sensitive marker for the identification of hemoglobin (Hb) variants. In this study, we aimed to examine two patients from two Chinese families who showed elevated Hb A2 levels but did not show any signs of ß-thal. The HBB variants were analyzed using direct sequencing of HBB and in silico prediction analysis. Moreover, the family's genetic history was investigated. We examined two probands from different Chinese families with elevated Hb A2 levels who were not afflicted with ß-thal, although several nucleotide changes were found at codon 81 (CTC>CTA) (HBB: c.246C>A) in Family 1 and a compound heterozygosity for codon 40 (AGG>AAG) (HBB: c.122G>A) and IVS-II-478 (C>A) (HBB: c.316-373C>A) in Family 2. After investigating the genetic history of both families including the ß-thal aspect, we found that these mutations were not responsible for the elevated Hb A2 levels. It is rarely reported that high Hb A2 level is not indicative of ß-thal. In contrast, low or normal Hb A2 level is always found with ß-thal due to other molecular defects that mask their ß-thal genotype. Our results highlight the importance of considering the genetic factors related and unrelated to ß-thal to improve the accuracy of future genetic counseling.
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Hemoglobina A2/análisis , Talasemia beta , China , Codón , Genotipo , Heterocigoto , Humanos , Mutación , Talasemia beta/diagnóstico , Talasemia beta/genéticaRESUMEN
BACKGROUND: Multiple morphological abnormalities of the sperm flagella (MMAF) is one kind of severe asthenozoospermia, which is caused by dysplastic development of sperm flagella. In our study, we sought to investigate the novel gene mutations leading to severe asthenozoospermia and MMAF. METHODS AND MATERIALS: The patient's spermatozoa were tested by Papanicolaou staining and transmission electron microscopy. Whole exome sequencing was performed on the patient with severe asthenozoospermia and MMAF. Sanger sequencing verified the mutations in the family. The expression of DNAH17 was detected by immunofluorescence and Western blot. RESULTS: Spermatozoa sample from the patient showed severe asthenozoospermia and MMAF. We detected biallelic mutations (c.C4445T, p.A1482V and c.C6857T, and p.S2286L) in DNAH17 (MIM:610063). The protein expression of DNAH17 was almost undetectable in spermatozoa from the patient with the biallelic mutations. CONCLUSION: These results demonstrated that DNAH17 may be involved in severe asthenozoospermia and MMAF.
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Astenozoospermia/genética , Dineínas Axonemales/genética , Cola del Espermatozoide/patología , Adulto , Alelos , Secuencia de Aminoácidos , Análisis Mutacional de ADN , Genes Recesivos , Humanos , Masculino , Linaje , Espermatozoides/patología , Espermatozoides/ultraestructura , Secuenciación del ExomaRESUMEN
Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by recurrent respiratory infections, nasosinusitis, tympanitis, and/or male infertility, all of which can severely impair the patient's quality of life. Multiple morphological abnormalities of the sperm flagella (MMAF) is one type of severe teratozoospermia and results from a variety of flagellar defects. In this study, we conducted whole-exome sequencing to identify and evaluate the genetic lesions in two patients with potential PCD and MMAF. Biallelic mutations in exon 10, c.983G>A; p.(Gly328Asp), and exon 29, c.3532G>A; p.(Asp1178Asn), of the CFAP74 (NM_001304360) gene were identified in patient 1 (P1), and biallelic mutations in exon 7, c.652C>T; p.(Arg218Trp), and exon 35, c. 4331G>C; p.(Ser1444Thr), of the same gene were identified in patient 2 (P2). Bioinformatic analysis suggested that these variants may be disease causing. Immunofluorescence confirmed that CFAP74 was absent in these patients' sperm samples. Intracytoplasmic sperm injection (ICSI) was carried out for P1, and his wife became pregnant after embryo transfer and gave birth to a healthy baby. To the best of our knowledge, this study is the first to identify the importance of CFAP74 in potential PCD and MMAF, contributing to the genetic diagnosis of these disorders and helping to predict pregnancy outcomes relevant in in vitro fertilization.
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Anomalías Múltiples/genética , Trastornos de la Motilidad Ciliar/genética , Infertilidad Masculina/genética , Teratozoospermia/genética , Anomalías Múltiples/patología , Adulto , Alelos , Trastornos de la Motilidad Ciliar/complicaciones , Trastornos de la Motilidad Ciliar/patología , Femenino , Flagelos/genética , Flagelos/patología , Predisposición Genética a la Enfermedad , Humanos , Infertilidad Masculina/complicaciones , Infertilidad Masculina/patología , Masculino , Mutación/genética , Cola del Espermatozoide/metabolismo , Cola del Espermatozoide/patología , Espermatozoides/anomalías , Espermatozoides/metabolismo , Teratozoospermia/complicaciones , Teratozoospermia/patología , Secuenciación del ExomaRESUMEN
It is widely recognized that microhaps are powerful markers for different forensic purposes, mainly due to their advantages of both short tandem repeats and single nucleotide polymorphisms, including multiple alleles, low mutation rate, and absence of stutter peaks. In the present study, a panel of 60 microhap loci was developed and utilized in forensic kinship analysis as a preliminary study. Genotyping of microhap was performed by massively parallel sequencing and haplotypes were directly achieved from sequence reads of 73 samples from Chinese Han population. We observed that 49 out of 60 loci have effective number of alleles greater than 3.0 and 10 out of 60 have values above 4.0, with an average value of 3.5598. The heterozygosity values were in a range from 0.5840 to 0.8546 with an average of 0.7268 and the cumulative power of exclusion value of the 60 loci is equal to 1-4.78 × 10-18 . Moreover, we demonstrated the applicability of this method by different relationship inference problems, including identification of single parent-offspring, full-sibling, and second-degree relative. The results indicated that the assembled microhap panel provided more power for relationship inference, than commonly used short tandem repeats or single nucleotide polymorphism system.
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Haplotipos/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Repeticiones de Microsatélite/genética , Pueblo Asiatico/genética , Humanos , Polimorfismo de Nucleótido Simple/genéticaRESUMEN
SNPs, combined with massively parallel sequencing technology, have proven applicability in noninvasive prenatal paternity testing (NIPPT) for singleton pregnancies in our previous research, using circulating cell-free DNA in maternal plasma. However, the feasibility of NIPPT in twin pregnancies has remained uncertain. As a pilot study, we developed a practical method to noninvasively determine the paternity of twin pregnancies by maternal plasma DNA sequencing based on a massively parallel sequencing platform. Blood samples were collected from 15 pregnant women (twin pregnancies at 9-18 weeks of gestation). Parental DNA and maternal plasma cell-free DNA were analyzed with custom-designed probes covering 5226 polymorphic SNP loci. A mathematical model for data interpretation was established, including the zygosity determination and paternity index calculations. Each plasma sample was independently tested against the alleged father and 90 unrelated males. As a result, the zygosity in each twin case was correctly determined, prior to paternity analysis. Further, the correct biological father was successfully identified, and the paternity of all 90 unrelated males was excluded in each case. Our study demonstrates that NIPPT can be performed for twin pregnancies. This finding may contribute to development in NIPPT and diagnosis of certain genetic diseases.
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Ácidos Nucleicos Libres de Células , Medicina Legal/métodos , Paternidad , Embarazo Gemelar/genética , Gemelos , Ácidos Nucleicos Libres de Células/sangre , Ácidos Nucleicos Libres de Células/clasificación , Ácidos Nucleicos Libres de Células/genética , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Proyectos Piloto , Polimorfismo de Nucleótido Simple/genética , Embarazo , Análisis de Secuencia de ADN , Gemelos/clasificación , Gemelos/genéticaRESUMEN
BACKGROUND: Multiple morphological abnormalities of the sperm flagella (MMAF) is a kind of severe teratozoospermia. Patients with the MMAF phenotype are infertile and present aberrant spermatozoa with absent, short, coiled, bent and/or irregular flagella. Mutations in several genes can explain approximately 30%-50% of MMAF cases and more genetic pathogenies need to be explored. SPEF2 was previously demonstrated to play an essential role in sperm tail development in mice and pig. Dysfunctional mutations in SPEF2 impair sperm motility and cause a short-tail phenotype in both animal models. OBJECTIVE: Based on 42 patients with severe infertility and MMAF phenotype, we explored the new genetic cause of human MMAF phenotype. METHODS AND RESULTS: By screening gene variants in 42 patients with MMAF using whole exome sequencing, we identified the c. 12delC, c. 1745-2A > G, c. 4102 G > T and c. 4323dupA mutations in the SPEF2 gene from two patients. Both of these mutations are rare and potentially deleterious. Transmission electron microscope (TEM) analysis showed a disrupted axonemal structure with mitochondrial sheath defects in the patients' spermatozoa. The SPEF2 protein level was significantly decreased in the spermatozoa of the patients revealed by Western blot (WB) and immunofluorescence (IF) analyses. CONCLUSION: Our experimental findings indicate that loss-of-function mutations in the SPEF2 gene can cause the MMAF phenotype in human.
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Anomalías Múltiples/genética , Proteínas de Ciclo Celular/genética , Infertilidad Masculina/genética , Mutación con Pérdida de Función , Anomalías Múltiples/diagnóstico por imagen , Axonema/patología , Humanos , Infertilidad Masculina/diagnóstico por imagen , Masculino , Fenotipo , Motilidad Espermática/genética , Cola del Espermatozoide/patología , Espermatozoides/patología , Secuenciación del ExomaRESUMEN
Chromosomal microdeletions and microduplications have been proven to be a significant proportion of genetic factors underlying birth defects. Chromosomal microarray analysis (CMA) and next generation sequencing-based copy number variation (CNV-seq) assay have been recommended as first-tier tests for prenatal evaluation of disease-causing CNV across the genome. With the broad application of such technologies in prenatal genetic diagnosis, there is a needed to enhance the consistency in interpretation and reporting of CNV results in clinical laboratories across China. In addition, a standard guideline for prenatal analysis and reporting of regions of homozygosity (ROH) is also required. To assist the classification, interpretation and reporting of CNV/ROH, the following recommendations have been developed, which may enhance a standard application of CMA/CNV-seq techniques in prenatal genetic diagnosis.
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Variaciones en el Número de Copia de ADN , Diagnóstico Prenatal , China , Consenso , Femenino , Homocigoto , Humanos , EmbarazoRESUMEN
OBJECTIVE: To explore the clinical and genetic characteristics of a patient with 17-hydroxylase/17,20-lyase deficiency. METHODS: The patient was infertile without contraception. Laboratory examination showed her chromosomal karyotype to be 46, XX. DNA sequencing was performed to detect variants of CYP17A1 gene in the patient and her family members. RESULTS: Sanger sequencing revealed that the patient has carried homozygous variant c.1486C>T in the exon 8 of the CYP17A1 gene, which resulted in substitution of arginine by cysteine (p.Arg496Cys). Her family members were all heterozygotes for the same variant. CONCLUSION: Homozygous variant of the CYP17A1 gene c.1486C>T probably underlay the 17-hydroxylase deficiency in this patient. Above finding has enabled accurate genetic counseling and prenatal diagnosis for her family.
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Hiperplasia Suprarrenal Congénita , Esteroide 17-alfa-Hidroxilasa , Hiperplasia Suprarrenal Congénita/diagnóstico , Hiperplasia Suprarrenal Congénita/genética , Femenino , Pruebas Genéticas , Heterocigoto , Homocigoto , Humanos , Mutación , Esteroide 17-alfa-Hidroxilasa/genéticaRESUMEN
With the rapid development and adaptation of high-throughput sequencing in clinical settings, application of exome sequencing (ES) has been gradually expanded from pediatric to prenatal diagnosis in recent years. There is an urgent need to establish criteria for clinical grade ES in order to facilitate such a complex testing. The standardization of pre- and post-test consultation, quality control for sample processing process and validation of bioinformatics data analysis, and more importantly data interpretation and reporting, as well as appropriate reporting scope, is of great importance for health care stakeholders. To achieve this, a committee composed of a wide range of healthcare professionals has proposed an ES standard for prenatal diagnosis. This has provided expert opinion on the genetic counseling and reporting standards of prenatal ES for the purpose of applying ES technology in prenatal setting.
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Secuenciación del Exoma , Exoma , Diagnóstico Prenatal , Consenso , Exoma/genética , Femenino , Asesoramiento Genético , Pruebas Genéticas , Humanos , EmbarazoRESUMEN
BACKGROUND: Upper gastrointestinal cancers (including oesophageal cancer and gastric cancer) are the most common cancers worldwide. Artificial intelligence platforms using deep learning algorithms have made remarkable progress in medical imaging but their application in upper gastrointestinal cancers has been limited. We aimed to develop and validate the Gastrointestinal Artificial Intelligence Diagnostic System (GRAIDS) for the diagnosis of upper gastrointestinal cancers through analysis of imaging data from clinical endoscopies. METHODS: This multicentre, case-control, diagnostic study was done in six hospitals of different tiers (ie, municipal, provincial, and national) in China. The images of consecutive participants, aged 18 years or older, who had not had a previous endoscopy were retrieved from all participating hospitals. All patients with upper gastrointestinal cancer lesions (including oesophageal cancer and gastric cancer) that were histologically proven malignancies were eligible for this study. Only images with standard white light were deemed eligible. The images from Sun Yat-sen University Cancer Center were randomly assigned (8:1:1) to the training and intrinsic verification datasets for developing GRAIDS, and the internal validation dataset for evaluating the performance of GRAIDS. Its diagnostic performance was evaluated using an internal and prospective validation set from Sun Yat-sen University Cancer Center (a national hospital) and additional external validation sets from five primary care hospitals. The performance of GRAIDS was also compared with endoscopists with three degrees of expertise: expert, competent, and trainee. The diagnostic accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of GRAIDS and endoscopists for the identification of cancerous lesions were evaluated by calculating the 95% CIs using the Clopper-Pearson method. FINDINGS: 1â036â496 endoscopy images from 84â424 individuals were used to develop and test GRAIDS. The diagnostic accuracy in identifying upper gastrointestinal cancers was 0·955 (95% CI 0·952-0·957) in the internal validation set, 0·927 (0·925-0·929) in the prospective set, and ranged from 0·915 (0·913-0·917) to 0·977 (0·977-0·978) in the five external validation sets. GRAIDS achieved diagnostic sensitivity similar to that of the expert endoscopist (0·942 [95% CI 0·924-0·957] vs 0·945 [0·927-0·959]; p=0·692) and superior sensitivity compared with competent (0·858 [0·832-0·880], p<0·0001) and trainee (0·722 [0·691-0·752], p<0·0001) endoscopists. The positive predictive value was 0·814 (95% CI 0·788-0·838) for GRAIDS, 0·932 (0·913-0·948) for the expert endoscopist, 0·974 (0·960-0·984) for the competent endoscopist, and 0·824 (0·795-0·850) for the trainee endoscopist. The negative predictive value was 0·978 (95% CI 0·971-0·984) for GRAIDS, 0·980 (0·974-0·985) for the expert endoscopist, 0·951 (0·942-0·959) for the competent endoscopist, and 0·904 (0·893-0·916) for the trainee endoscopist. INTERPRETATION: GRAIDS achieved high diagnostic accuracy in detecting upper gastrointestinal cancers, with sensitivity similar to that of expert endoscopists and was superior to that of non-expert endoscopists. This system could assist community-based hospitals in improving their effectiveness in upper gastrointestinal cancer diagnoses. FUNDING: The National Key R&D Program of China, the Natural Science Foundation of Guangdong Province, the Science and Technology Program of Guangdong, the Science and Technology Program of Guangzhou, and the Fundamental Research Funds for the Central Universities.
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Algoritmos , Inteligencia Artificial , Endoscopía/métodos , Neoplasias Gastrointestinales/diagnóstico , Procesamiento de Imagen Asistido por Computador/métodos , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Casos y Controles , Niño , Femenino , Estudios de Seguimiento , Humanos , Masculino , Persona de Mediana Edad , Pronóstico , Estudios Prospectivos , Curva ROC , Estudios Retrospectivos , Adulto JovenRESUMEN
Multiple morphological abnormalities of flagella (MMAF) is one kind of severe teratozoospermia. Gene mutations reported in previous works only revealed the pathogenesis of approximately half of the MMAF cases, and more genetic defects in MMAF need to be explored. In the present study, we performed a genetic analysis on Han Chinese men with MMAF using whole-exome sequencing. After filtering out the cases with known gene mutations, we identified five novel mutation sites in the DNAH2 gene in three cases from three families. These mutations were validated through Sanger sequencing and absent in all control individuals. In silico analysis revealed that these DNAH2 variations are deleterious. The spermatozoa with DNAH2 mutations showed severely disarranged axonemal structures with mitochondrial sheath defection. The DNAH2 protein level was significantly decreased and inner dynein arms were absent in the spermatozoa of patients. ICSI treatment was performed for two MMAF patients with DNAH2 mutations and the associated couples successfully achieved pregnancy, indicating good nuclear quality of the sperm from the DNAH2 mutant patients. Together, these data suggest that the DNAH2 mutation can cause severe sperm flagella defects that damage sperm motility. These results provide a novel genetic pathogeny for the human MMAF phenotype.
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Dineínas Axonemales/genética , Estudios de Asociación Genética , Mutación/genética , Cola del Espermatozoide/patología , Teratozoospermia/genética , Secuencia de Bases , Secuencia de Consenso , Dineínas/metabolismo , Femenino , Humanos , Masculino , Linaje , Fenotipo , Semen/metabolismo , Motilidad Espermática , Cola del Espermatozoide/ultraestructura , Secuenciación del ExomaRESUMEN
OBJECTIVE: To determine the nature and origin of aberrant chromosomes in a child with multiple anomalies and psychomotor retardation. METHODS: Routine G-banding was carried out to analyze the karyotypes of the patient and his parents, and next generation sequencing for copy number variations (CNV-seq) was used for the fine mapping of the aberrant chromosomal regions. RESULTS: The proband and his uncle exhibited psychomotor retardation, craniofacial malformation, infantile external genitalia, and concealed penis. Cytogenetic analysis indicated that the child has a 46,XYqh+,+(9),t(9;13)(q13;q12),pat,-13 karyotype. His uncle was XYqh+,+(9),t(9;13)(q13;q12)mat,-13, his father was 46,XYqh+,t(9;13)(q13;q12)mat, his grandmother was 46,XX,t(9;13)(q13;q12), and his grandfather was 46,XYqh+. The result of CNV-seq assay for the child was 46,XY,+9p(pter-p13.2,-40 Mb×3). No deletion was detected. CONCLUSION: The partial trisomy 9 and partial monosomy 13 probably underlie the phenotypic abnormalities in the child. Combined chromosomal karyotyping and DNA sequencing can facilitate delineation of the nature and origin of the aberrant chromosomes.
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Anomalías Múltiples , Trisomía , Niño , Deleción Cromosómica , Cromosomas Humanos Par 13 , Cromosomas Humanos Par 9 , Variaciones en el Número de Copia de ADN , Humanos , Cariotipificación , Masculino , Monosomía , Linaje , Translocación GenéticaRESUMEN
BACKGROUND: Testis-expressed gene 11 (TEX11) is an X-linked gene and essential for meiotic recombination and chromosomal synapsis. TEX11 deficiency causes meiotic arrest and male infertility, and many TEX11 mutations have been found in azoospermic and infertile men. CASE PRESENTATION: This study reported one novel TEX11 mutation (2653G â T, in exon 29, GenBank accession number, NM_031276) in two brothers with azoospermia. This mutation was firstly screened out by whole-exome sequencing (WES) and further verified by amplifying and sequencing the specific exon 29. Surprisingly, the same exonic missense mutation (W856C) was observed in two brothers but not in their mother. Histological analysis of testicular biopsy from both brothers revealed meiotic arrest and no post-meiotic round spermatids and mature spermatozoa were observed in the seminiferous tubules. TEX11 expression was observed strongly in spermatogonia and weakly in spermatocytes, but not in Sertoli cells and interstitial cells. CONCLUSIONS: We identified one novel TEX11 mutation in two brothers and summarized the literature regarding TEX11 mutations and male infertility. This study and previous literature indicate that TEX11 mutations are closely associated with male infertility, especially azoospermia, although auxiliary clinical analyses are needed to figure out the causes of male infertility.
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Azoospermia/genética , Proteínas Cromosómicas no Histona/genética , Secuenciación del Exoma/métodos , Mutación Missense , Adulto , Azoospermia/patología , Biopsia , Proteínas de Ciclo Celular , Femenino , Humanos , Masculino , Meiosis , Linaje , HermanosRESUMEN
BACKGROUND: Recent advances in massively parallel sequencing (MPS) technology have provided efficient methods for noninvasive prenatal paternity testing (NIPAT). However, a well-accepted protocol has not been established. The present study developed an MPS-based approach for NIPAT and compared the performance of two recently reported methods for MPS data interpretation. STUDY DESIGN AND METHODS: We selected 1795 unlinked polymorphic single-nucleotide polymorphisms (SNPs) and performed paternity analysis in 34 real parentage test cases with maternal plasma samples using the Illumina HiSeq platform. Sequencing data were interpreted by the straightforward counting method for the identification of paternal alleles and mathematical algorithms for paternity index (PI) calculation, respectively. RESULTS: Based on the sequencing data from each family case, both of the two statistical approaches produced a significant separation between the biological father and 90 unrelated males (p < 0.0001) when sufficient effective loci were attained. Nevertheless, up to 30.82% of real paternal alleles were filtered by a predefined cutoff and resulted in insufficient effective loci, especially in plasma samples with low fetal fraction (approx. 90.60% were filtered). In contrast, the PI calculation model utilized all maternal homozygous SNPs as effective loci (approx. 40% of total SNPs) and successfully identified the correct biological father, with the log-transformed combined PI (Lg(CPI)) value varying from 68.23 to 158.01 in each family case. CONCLUSION: Our study illustrates that the Bayesian approach represents the better choice in NIPAT data interpretation. Further, the adoption of more informative markers (e.g., tri-allelic SNPs, tetra-allelic SNPs, and micro-haplotypes) or deeper sequencing is recommended for the improvement of the testing efficiency.
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Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Paternidad , Alelos , Femenino , Genotipo , Humanos , Polimorfismo de Nucleótido Simple/genética , Embarazo , Análisis de Secuencia de ADN/métodosRESUMEN
Researchers have sought to develop an effective protocol for paternity analysis using cell-free DNA (cfDNA) in maternal plasma. The use of massively parallel sequencing (MPS) technology for SNP testing is attractive because of its high-throughput capacity and resolution to single-base precision. In this study, we designed a customized SNP panel for cfDNA sequencing that includes 720 short amplicons (< 140 bp) targeting SNPs on the autosome and Y chromosome. The systemic performance was evaluated using the Ion Torrent PGM, indicating balanced coverage among most of the included loci, except for 78 poorly performing SNPs that were observed to have an inconsistent allele balance, lower coverage reads or high background signals. Then, the custom panel was used to perform cfDNA genotyping in maternal plasma from 20 pregnancies in the first and second trimesters (9 to 21 weeks). By establishing an allele fraction cutoff of 2.0%, 53 to 128 autosomal SNP loci were considered informative for paternal origin. Validation results in foetal samples showed that 49.43% to 100% of the real paternal alleles were accurately identified, with incorrect alleles encountered in 3 cases. The concentration of foetal cfDNA ranged from 4.28% to 10.70%. Our results show that this amplicon-based sequencing strategy could be utilized in analysing paternally inherited alleles in maternal plasma. However, further studies and optimization are required for a more detailed and accurate interpretation of the cfDNA sequencing results based on MPS technology.
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Alelos , Secuenciación de Nucleótidos de Alto Rendimiento/instrumentación , Polimorfismo de Nucleótido Simple , Embarazo/sangre , Ácidos Nucleicos Libres de Células , Femenino , Feto , Genotipo , Humanos , Paternidad , Análisis de Secuencia de ADNRESUMEN
OBJECTIVE: To evaluate the incidence and characteristics of unusual twinning by using single nucleotide polymorphism (SNP) array to identify twin zygosity. METHODS: This study reviewed 386 twin pairs who were seen for prenatal or postnatal diagnosis and underwent SNP array to detect zygosity. RESULTS: The incidence of monozygotic (MZ) twins was 11.36% (25/220) in the assisted reproductive technology (ART)-conceived group. Monochorionic dizygotic twins represented 3 of 24 monochorionic ART-conceived twin pairs (3/24, 12.50%) but none in the spontaneous twin pairs. Among 4 single-embryo transfer twin pairs, 3 represented unusual twinning, including 2 MZ twin pairs with discordant karyotypes and 1 dizygotic twin pair of the same gender. Of the pregnancies with 2 or more embryos transferred, 7.77% (15/193) were MZ. Additionally, there was a dichorionic monozygotic twin pair with placental vascular anastomoses from a day-5 blastocyst transfer. CONCLUSION: Single nucleotide polymorphism array can provide zygosity diagnosis in addition to chromosomal copy number variation and uniparental disomy detection. ART twin pregnancies have a risk of unusual twinning, such as monochorionic dizygotic, single-embryo transfer twin pairs with discordant karyotypes or dizygotic, and dichorionic monozygotic with vascular anastomoses from day-5 transfer.