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single nucleotide polymorphism array (SNP-array) analysis for fetuses with abnormal nasal bone

ARCHIVES OF GYNECOLOGY AND OBSTETRICS 2024年第6期309卷 2475-2482页

作者： Xie, Xiaorui Su, Linjuan Li, Ying Shen, Qingmei Wang, Meiying Wu, Xiaoqing Fujian Med Univ Fujian Prov Matern & Childrens Hosp Med Genet Diag & Therapy Ctr Fujian Key Lab Prenatal Diag & Birth DefectAffili 18 Daoshan Rd Fuzhou 350001 Peoples R China

PurposeThis study aims to evaluate the prevalence of submicroscopic chromosomal abnormalities found on single nucleotide polymorphism array (SNP array) in pregnancies with either an absent or hypoplastic nasal *** retrospective study included 333 fetuses with either nasal bone hypoplasia or absence identified on prenatal ultrasound. SNP array analysis and conventional karyotyping were performed in all the subjects. The prevalence of chromosomal abnormalities was adjusted for maternal age and other ultrasound findings. Fetuses with either an isolated nasal bone absence or hypoplasia, those that had additional soft ultrasound markers, and those where structural defects were found on ultrasound were divided into three groups: A, B, and C, *** the total cohort of 333 fetuses, 76 (22.8%) had chromosomal abnormalities, including 47 cases of trisomy 21, 4 cases of trisomy 18, 5 cases of sex chromosome aneuploidy, and 20 cases of copy number variations of which 12 were pathogenic or likely pathogenic. The prevalence of chromosomal abnormalities in group A (n = 164), B (n = 79), and C (n = 90) was 8.5%, 29.1% and 43.3%, respectively. The incremental yields by SNP-array compared with karyotyping in group A, B, and C were 3.0%, 2.5% and 10.7%, respectively (p > 0.05). Compared to karyotype analysis, SNP array detected an additional 2 (1.2%), 1 (1.3%), and 5 (5.6%) pathogenic or likely pathogenic CNVs in groups A, B, and C, respectively. In the 333 fetuses, the prevalence of chromosomal abnormalities in women with advanced maternal age (AMA) was significantly higher than that in non-AMA women, (47.8% vs. 16.5%, p < 0.05).ConclusionIn addition to Down's syndrome, many other chromosomal abnormalities are present in fetuses with abnormal nasal bone. SNP array can improve the prevalence of chromosomal abnormalities associated with nasal bone abnormalities, especially in pregnancies with non-isolated nasal bone abnormalities and advanced maternal a

关键词： Nasal bone absence Nasal bone hypoplasia Karyotyping single nucleotide polymorphism array Copy number variations

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Pedigree reconstruction for triploid apple cultivars using single nucleotide polymorphism array data

PLANTS PEOPLE PLANET

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PLANTS PEOPLE PLANET 2023年第1期5卷 98-111页

作者： Howard, Nicholas P. Micheletti, Diego Luby, James J. Durel, Charles-Eric Denance, Caroline Muranty, Helene Ordidge, Matthew Albach, Dirk C. Carl von Ossietzky Univ Oldenburg Inst Biol & Umweltwissensch Oldenburg Germany Univ Minnesota Dept Hort Sci St Paul MN 55108 USA Fdn Edmund Mach San Michele All Adige TN Italy Univ Angers Inst Agro SFR QuaSaV INRAEIRHS Angers France Univ Reading Sch Agr Policy & Dev Reading Berks England

Societal Impact Statement Many economically, culturally, and historically important apple cultivars are triploids, which have three copies of each chromosome instead of the more typical two copies in diploids. Despite their prevalence and importance, there have been conflicting reports regarding their origin and their ability to beget diploids. New genetic analysis methodologies outlined in this study have clarified the genetic origin of triploid apple cultivars and suggest that triploidy has been a dead end in historic apple pedigrees. The specific results of this study have resolved the pedigrees of many cultivars, including the famous English cultivar Cox's Orange Pippin and the oldest known US cultivar Roxbury Russet. In apple (Malus x domestica), most cultivars are diploid, though a sizeable number are triploids, which tend to be stronger growing, more robust, and bear larger fruit. However, triploidy is also associated with strongly reduced fertility. Some recorded pedigrees for historical apple cultivars include triploids as parents of diploids, despite this reputation of poor fertility. This information, coupled with some initiatives using triploids in breeding efforts, result in confusion about how possible or common it is for triploids to be parents of diploid offspring. To date, no studies have systematically evaluated and identified pedigrees of triploid apple cultivars to resolve these contradictions. Here, we describe a method to make triploid genotype calls using Illumina Infinium single nucleotide polymorphism (SNP) array data through a novel Python script: ploidyClassifier. SNP data for 219 unique triploids was compared alongside 2498 unique diploid apple accessions to conduct pedigree reconstruction. Unreduced gamete-donating parents were identified for over half of the triploid accessions. From those, reduced gamete-donating parents were identified for nearly half. Full or partial pedigrees for many classic triploids were uncovered, including that

关键词： apple genetics Malus pedigree reconstruction polyploidy single nucleotide polymorphism array triploid

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single nucleotide polymorphism array analysis for fetuses from balanced translocation carriers at the second trimester

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Heliyon 2024年第20期10卷 e38387页

作者： Wu, Xiaoqing Du, Shengrong Liang, Bin Su, Linjuan Li, Ying Chen, Yuqin Zheng, Lin Lin, Na Huang, Hailong Xu, Liangpu Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics Fujian Medical University Fujian Fuzhou China Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect Fujian Fuzhou China Department of Laboratory Medicine Fujian Medical University Fujian Fuzhou China Key Laboratory of Clinical Laboratory Technology for Precision Medicine (Fujian Medical University) Fujian Province University Fujian Fuzhou China

Prenatal diagnosis is crucial for pregnancies from couples with a carrier of a balanced translocation. We retrospectively reviewed 195 pregnancies from 189 couples with a balanced translocation carrier. Of these, 126 were from natural conception, while 69 were conceived through assisted reproductive technology (ART) with preimplantation genetic diagnosis (PGD). Both single nucleotide polymorphism (SNP) array analysis and conventional karyotyping were conducted on all pregnancies, and karyotype-visible imbalances and pathogenic/likely pathogenic copy number variations (CNVs) were categorized as clinically significant abnormalities. In natural conception group, couples with a female carrier experiencing more than two miscarriages accounted for 30.2 %, significantly higher than the 14.0 % in male carrier couples (p < 0.05). In the PGD group, similar difference was observed between female and male carrier couples (p < 0.05). In the natural pregnancies, SNP array analysis yielded additional 12 cases of CNVs, including two cases of pathogenic (P)/likely pathogenic (LP) aberrations, four variants with uncertain significance (VUS), and six likely benign variants. Only two CNVs were found to be associated with translocation breakpoints, which were finally confirmed to be of parental inheritance. In the PGD pregnancies, two cases of VUS unrelated to the translocation breakpoints were revealed. Taken together, repeated miscarriage was more frequently observed in couples where the carrier was female than male. Conventional SNP array analysis in prenatal diagnosis indicated insufficient evidence to support the notion that balanced translocations increase the likelihood of fetuses having clinically significant CNVs. © 2024

关键词： Balanced translocation Conventional karyotyping Copy number variants single nucleotide polymorphism array Translocation breakpoints

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single nucleotide polymorphism array analysis of 102 patients with developmental delay and/or intellectual disability from Fujian, China

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CLINICA CHIMICA ACTA 2020年 510卷 638-643页

作者： Liang, Bin Wang, Yan Lin, Na Huang, Hailong Chen, Lingji Chen, Meihuan Yu, Donghong Chen, Xuemei He, Deqin Xu, Liangpu Fujian Med Univ Fujian Matern & Child Hlth Hosp Fujian Key Lab Prenatal Diag & Birth Defect Affiliated Hosp Fuzhou 350001 Peoples R China Fujian Med Univ Fujian Matern & Child Hlth Hosp Med Res Ctr Affiliated Hosp Fuzhou 350001 Peoples R China

Developmental delay/intellectual disability (DD/ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In this study, we evaluated the usefulness of single nucleotide polymorphism (SNP) array in the detection of genetic causes of 102 DD/ID patients from Fujian (China). Of them, clinically relevant variants (including pathogenic and likely pathogenic), variants of uncertain significance (VOUS), and no clinically relevant variants (including likely benign and benign) were detected in 19, 4 and 79 patients, accounting for 18.6%, 3.9% and 77.5%, respectively, with a diagnostic yield of 18.6% in our study. Furthermore, we divided 19 clinically relevant variants into 4 groups, including chromosome aneuploidy (n = 1);large copy number variants (CNVs) (> 10 Mb) (n = 8);known genomic disorders (n = 8), and likely pathogenic CNVs (n = 2). Moreover, we discussed our findings with respect to 4 cases of VOUS. Overall, we confirmed that DD/ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide SNP array in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with causal chromosomal aberrations, and discussed the potential implication in DD/ID of genes located within those CNVs or regions of homozygosity.

关键词： Developmental delay Intellectual disability single nucleotide polymorphism array Copy number variant Region of homozygosity

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Clinical findings and genetic analysis of patients with copy number variants involving 17p13.3 using a single nucleotide polymorphism array: a single-center experience

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BMC MEDICAL GENOMICS 2022年第1期15卷 268-268页

作者： Liang, Bin Yu, Donghong Zhao, Wantong Wang, Yan Wu, Xiaoqing Chen, Lingji Lin, Na Huang, Hailong Xu, Liangpu Fujian Med Univ Fujian Matern & Child Hlth Hosp Coll Clin Med Obstet & Gynecol & Pediat Med Genet Diag & Therapy CtrFujian Key Lab Prenat Fuzhou 350001 Peoples R China Fujian Obstet & Gynecol Hosp Fuzhou 350011 Fujian Peoples R China Fujian Med Univ Fujian Matern & Child Hlth Hosp Coll Clin Med Obstet & Gynecol & Pediat Med Res Ctr Fuzhou 350001 Peoples R China

Background: 17p13.3 microdeletions or microduplications (collectively known as copy number variants or CNVs) have been described in individuals with neurodevelopmental disorders. However, 17p13.3 CNVs were rarely reported in fetuses. This study aims to investigate the clinical significance of 17p13.3 CNVs with varied sizes and gene content in prenatal and postnatal samples. Methods: Eight cases with 17p13.3 CNVs out of 8806 samples that had been subjected to single nucleotide polymorphism array analysis were retrospectively analyzed, along with karyotyping, clinical features, and follow-up. Results: Eight cases with 17p13.3 CNVs consisted of five fetuses, one aborted embryo and two probands manifested severe congenital defects. The indications of prenatal testing varied considerably for the five fetuses, including ultrasound abnormalities (n = 3), segmental deletions indicated by non-invasive prenatal testing (n = 1), and intellectual disability in the mother of one fetus (n = 1). Of them, two and six harbored copy number gains and losses involving 17p13.3, respectively. The size of the detected 17p13.3 CNVs ranged from 576 kb to 5.7 Mb. Case 1 was diagnosed with 17p13.3 duplication syndrome, and cases 4, 6, and 7 with Miller-Dieker syndrome (MDS). Microdeletions of the 17p13.3 region in two cases (cases 5 and 8) involving YWHAE and CRK, sparing PAFAH1B1, were classified as pathogenic. Case 2 harbored a 576 kb microduplication, encompassing YWHAE and CRK but not PAFAH1B1, which was of maternal origin and considered a variant of uncertain significance. Case 3 carried one 74.2 Mb mosaic duplication of approximately 3.5 on chromosome 17p13.2q25.3, and two deletions at 17p13.3p13.2 and 17q25.3. The karyotype of case 3 was 46,XY,r(17)(p13q25). For five fetuses, only case 2 continued gestation and showed normal development at the age of 15 months;the others were subjected to termination of pregnancy. Conclusion: The clinical findings of 17p13.3 microdeletions or microdupl

关键词： Miller-Dieker syndrome 17p13.3 Duplication syndrome CNV involving 17p13.3 single nucleotide polymorphism array Genetic analysis

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Prenatal diagnosis of 22q11.2 copy number abnormalities in fetuses via single nucleotide polymorphism array

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MOLECULAR BIOLOGY REPORTS 2020年第10期47卷 7529-7535页

作者： Cai, Meiying Lin, Na Su, Linjuan Wu, Xiaoqing Xie, Xiaorui Li, Ying Lin, Yuan Huang, Hailong Xu, Liangpu Fujian Med Univ Fujian Key Lab Prenatal Diag & Birth Defect Fujian Matern & Child Hlth Hosp Dept Prenatal Diag CtrAffiliated Hosp Fuzhou Peoples R China

The q11.2 region on chromosome 22 contains numerous low-copy repeats that lead to deleted or duplicated regions in the chromosome, thereby resulting in different syndromes characterized by intellectual disabilities or congenital anomalies. The association between patient phenotypes and 22q11.2 copy number abnormalities has been previously described in postnatal cases;however, these features have not been systematically evaluated in prenatal cases because of limitations in phenotypic identification in prenatal testing. In this study, we investigated the detection rate of 22q11.2 copy number abnormalities in 2500 fetuses using single nucleotide polymorphism (SNP) array and determined the common abnormal ultrasound findings in fetuses carrying the 22q11.2 copy number abnormalities. The 22q11.2 copy number abnormalities were identified in 13 fetuses with cardiovascular malformations (6/13), kidney malformations (3/13), isolated ultrasound markers (3/13), or high-risk Down syndrome based on maternal serum screening (1/13). Approximately 0.5% (13/2500) of the fetuses harbored 22q11.2 copy number abnormalities. The most frequent ultrasound findings in fetuses with these abnormalities were cardiovascular malformations, followed by kidney malformations and isolated ultrasound markers. Prenatal diagnosis of these genetic abnormalities allows for the delineation of differential diagnoses, characterization of a wide spectrum of associated malformations, and determination of associations that exist between prenatal diagnosis and obstetrical outcomes.

关键词： 22q11 2 copy number abnormality single nucleotide polymorphism array Prenatal diagnosis Genomic diseases

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An extragonadal yolk sac tumor presumed to be of postmeiotic germ cell origin by genetic zygosity analysis via single nucleotide polymorphism array

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GENES CHROMOSOMES & CANCER 2020年第3期59卷 209-213页

作者： Tamura, Daisuke Maeda, Daichi Sato, Toshiharu Sugawara, Tae Shirasawa, Hiromitsu Shimizu, Dai Sato, Naoki Goto, Akiteru Terada, Yukihiro Akita Univ Grad Sch Med Dept Obstet & Gynecol 1-1-1 Hondo Akita Akita 0108543 Japan Akita Red Cross Hosp Dept Gynecol Akita Japan Osaka Univ Grad Sch Med Dept Clin Genom Osaka Japan Akita Univ Grad Sch Med Dept Cellular & Organ Pathol Akita Japan

An extragonadal yolk sac tumor (YST) is a rare malignant germ cell tumor that usually occurs in childhood. The pathogenesis of extragonadal YST remains largely unknown, especially with regards to its cell of origin. Herein, we report a case of extragonadal YST arising in the uterine round ligament. A 31-year-old Japanese woman, para 2, underwent partial resection of a left-sided, 5-cm, solid inguinal mass. Intraoperative findings showed enlargement of the uterine round ligament in the inguinal canal. Pathological evaluation diagnosed the mass as YST with a mature teratoma (MT) component. The preoperative alpha-fetoprotein level was markedly elevated, at 24 790 ng/mL. Postoperative magnetic resonance imaging revealed a right ovarian MT and a 3-cm mass remaining in the left lower abdominal wall. The patient underwent total abdominal hysterectomy, bilateral adnexectomy, and left inguinal mass resection. We sampled three frozen tissues (YST, right ovarian MT, and left normal ovary) and performed a single nucleotide polymorphism (SNP) array. Pathological evaluation revealed remnant extragonadal YST in the left inguinal region. The SNP array demonstrated a completely homozygous YST genotype. Copy number variations were gains of 1p, 1q, 2p, 3p, 7p, 8p, 10q, 14q, 18p, 20q, Xp, and Xq and losses of 12q, 20p, and Xq. The right ovarian MT and left normal ovary were partially homozygous and heterozygous, respectively. The evidence suggests that this neoplasm is presumed to be a postmeiotic germ cell origin.

关键词： extragonadal germ cell tumor genetic zygosity single nucleotide polymorphism array yolk sac tumor

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Analysis of somatic copy number alterations in biliary tract carcinoma using a single nucleotide polymorphism array

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FUTURE SCIENCE OA 2022年第1期8卷 FSO766页

作者： Shioi, Yoshihiro Osakabe, Mitsumasa Yanagawa, Naoki Nitta, Hiroyuki Sasaki, Akira Sugai, Tamotsu Iwate Med Univ Sch Med Dept Mol Diagnost Pathol 2-1-1 Shiwagun Yahaba Iwate 0283695 Japan Iwate Med Univ Sch Med Dept Surg 2-1-1 Shiwagun Yahaba Iwate 0283695 Japan

Lay abstract Biliary tract carcinoma, including gall bladder carcinoma (GBC) and biliary duct carcinoma (BDC), has a poor prognosis. Comprehensive genomic (single nucleotide polymorphism-array) profiling plays important roles in evaluation of the carcinogenesis of biliary tract carcinoma. In the hierarchical cluster analysis, two clusters were identified (subgroup 1 with low somatic copy number alterations [SCNAs] and subgroup 2 with high SCNAs);GBC was found to be predominant in subgroup 1, whereas BDC was predominant in subgroup 2. These findings suggested that GBC and BDC had different genetic backgrounds in terms of SCNAs. Aim: Biliary tract carcinoma (BTC), including gall bladder carcinoma (GBC) and biliary duct carcinoma (BDC), has a poor prognosis. Comprehensive genomic profiling has important roles in evaluation of the carcinogenesis of BTC. Materials & methods: We examined somatic copy number alterations (SCNAs) using a single nucleotide polymorphism array system to analyze 36 BTC samples (11 GBCs and 25 BDCs). Results: In hierarchical cluster analysis, two clusters were identified (subgroup 1 with low SCNAs and subgroup 2 with high SCNAs). GBC was predominant in subgroup 1, whereas BDC was predominant in subgroup 2, suggesting that GBC and BDC had different genetic backgrounds in terms of SCNAs. Conclusion: These findings could be helpful for establishing the molecular carcinogenesis of BTCs.

关键词： bile duct cancer biliary tract carcinoma carcinogenesis cluster analysis crypt isolation method gall bladder cancer molecular alteration prognosis single nucleotide polymorphism array somatic copy number alteration

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Prenatal diagnosis of 7 cases with uniparental disomy by utilization of single nucleotide polymorphism array

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MOLECULAR CYTOGENETICS 2021年第1期14卷 19-19页

作者： Zhou, Lili Zheng, Zhaoke Xu, Yunzhi Lv, Xiaoxiao Xu, Chenyang Xu, Xueqin Wenzhou Cent Hosp Ctr Prenatal Diag Wenzhou 325000 Peoples R China

Background The phenotypes of uniparental disomy (UPD) are variable, which may either have no clinical impact, lead to clinical signs and symptoms. Molecular analysis is essential for making a correct diagnosis. This study involved a retrospective analysis of 4512 prenatal diagnosis samples and explored the molecular characteristics and prenatal phenotypes of UPD using a single nucleotide polymorphism (SNP) array. Results Out of the 4512 samples, a total of seven cases of UPD were detected with an overall frequency of 0.16%. Among the seven cases of UPD, two cases are associated with chromosomal aberrations (2/7), four cases (4/7) had abnormal ultrasonographic findings. One case presented with iso-UPD (14), and two case presented with mixed hetero/iso-UPD (15), which were confirmed by Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as maternal UPD (15) associated with Prader-Willi syndrome (PWS). Four cases had iso-UPD for chromosome 1, 3, 14, and 16, respectively;this is consistent with the monosomy rescue mechanism. Another three cases presented with mixed hetero/isodisomy were consistent with a trisomy rescue mechanism. Conclusion The prenatal phenotypes of UPD are variable and molecular analysis is essential for making a correct diagnosis and genetic counselling of UPD. The SNP array is a useful genetic test in prenatal diagnosis cases with UPD.

关键词： uniparental disomy single nucleotide polymorphism array prenatal diagnosis

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Molecular delineation of small supernumerary marker chromosomes using a single nucleotide polymorphism array

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MOLECULAR CYTOGENETICS 2020年第1期13卷 19-19页

作者： Zhou, Lili Zheng, Zhaoke Wu, Lianpeng Xu, Chenyang Wu, Hao Xu, Xueqin Tang, Shaohua Wenzhou Cent Hosp Ctr Prenatal Diag Wenzhou 325000 Peoples R China Wenzhou Med Univ Sch Lab Med & Life Sci Key Lab Med Genet Wenzhou 325000 Peoples R China

Background Defining the phenotype-genotype correlation of small supernumerary marker chromosomes (sSMCs) remains a challenge in prenatal diagnosis. We karyotyped 20,481 amniotic fluid samples from pregnant women and explored the molecular characteristics of sSMCs using a single nucleotide polymorphism (SNP) array. Results Out of the 20,481 samples, 15 abnormal karyotypes with sSMC were detected (frequency: 0.073%) and the chromosomal origin was successfully identified by SNP array in 14 of them. The origin of sSMCs were mainly acrocentric-derived chromosomes and the Y chromosome. Two cases of sSMC combined with uniparental disomy (UPD) were detected, UPD(1) and UPD(22). More than half of the cases of sSMC involved mosaicism (8/15) and pathogenicity (9/15) in prenatal diagnosis. A higher prevalence of mosaicism for non-acrocentric chromosomes than acrocentric chromosomes was also revealed. One sSMC derived from chromosome 3 with a neocentromere revealed a 24.99-Mb pathogenic gain of the 3q26.31q29 region on the SNP array, which presented as an abnormal ultrasound indicating nasal bone hypoplasia. Conclusion The clinical phenotypes of sSMCs are variable and so further genetic testing and parental karyotype analysis are needed to confirm the characteristics of sSMCs. The SNP array used here allows a detailed characterisation of the sSMC and establishes a stronger genotype-phenotype correlation, thus allowing detailed genetic counselling for prenatal diagnosis.

关键词： Small supernumerary marker chromosome single nucleotide polymorphism array Prenatal diagnosis

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