Single Nucleotide Polymorphism Microarray Analysis Research Articles

Clinical application of single nucleotide polymorphism microarray analysis in pregnancy loss in Northwest China.

Background: Spontaneous abortion is the most common complication of early pregnancy. In this study, we aim to investigate the clinical application value of genetic diagnosis using single nucleotide polymorphism (SNP) microarray analysis on the products of conception and to characterize the types of genetic abnormalities and their prevalence in pregnancy loss in Northwest China. Methods: Over 48months, we selected 652 products of conception, which included chorionic villi, fetal tissues, germ cell samples, amniotic fluid samples, cord blood samples, and a cardiac blood sample. We analyzed the distribution of chromosomal abnormalities leading to fetal arrest or abortion using SNP array. The patients were then categorized divided into groups based on maternal age, gestational age, number of miscarriages, and maternal ethnic background. The incidences of various chromosomal abnormalities in each group were compared. Results: Of the 652 cases, 314 (48.16%) exhibited chromosomal abnormalities. These included 286 cases with numerical chromosomal abnormalities, 24 cases with copy number variation, and four cases with loss of heterozygosity. Among them, there were 203 trisomy cases, 55 monosomy cases, and 28 polyploidy cases. In the subgroup analysis, significant differences were found in the frequency of numerical chromosomal abnormalities and copy number variation between the advanced and younger maternal age group as well as between the early and late abortion groups. Furthermore, we identified significant differences in the frequency of numerical chromosomal abnormalities between the first spontaneous abortion and recurrent miscarriage groups. However, there were no significant differences in the frequency of numerical chromosomal abnormalities between the Han and Uighur groups. Conclusion: Our research highlights chromosomal abnormalities as the primary cause of spontaneous abortion, with a higher incidence in early pregnancy and among women of advanced age. The use of SNP array analysis emerges as an effective and reliable technique for chromosome analysis in aborted fetuses. This method offers a comprehensive and dependable genetic investigation into the etiology of miscarriage, establishing itself as a valuable routine selection for genetic analysis in cases of natural abortions.

Prenatal diagnosis of two fetuses with Xp22.31 microdeletion syndrome indicated by non-invasive prenatal testing

To assess the value of non-invasive prenatal testing (NIPT) for detecting fetal chromosomal microdeletion/microduplication syndromes by carrying out prenatal diagnoses for two fetuses with Xp22.31 microdeletion indicated by NIPT. Two pregnant women suspected for fetal Xp22.31 microdeletion syndrome who presented at Zaozhuang Maternal and Child Health Care Hospital on December 5, 2017 and October 15, 2020 were selected as the study subjects. Clinical data of the two women were collected, and peripheral venous blood samples were collected for NIPT testing. Amniotic fluid samples were taken for G-banding chromosomal karyotyping analysis and copy number variation sequencing (CNV-seq) for fetus 1, while G-banding chromosomal karyotyping and single nucleotide polymorphism microarray analysis (SNP array) were carried out for fetus 2. Peripheral venous blood samples of couple 1 were collected for CNV-seq to verify the origin of copy number variation . NIPT indicated that fetus 1 had harbored a 1.3 Mb deletion in the Xp22.31 region, while G-banding chromosomal karyotyping had found no abnormality. CNV-seq analysis verified the fetus to be seg[GRCh37]del(X)(p22.31)chrX:g.6800001_7940000del, with a 1.14 Mb deletion at Xp22.31, which was derived from its mother. NIPT indicated that fetus 2 had harbored a 1.54 Mb deletion in the Xp22.31 region, while G-banding chromosomal karyotyping had found no abnormality. SNP array analysis indicated arr[GRCh37]Xp22.31(6458940_8003247)×0, with a 1.54 Mb deletion in Xp22.31 region. NIPT not only has a good performance for detecting fetal trisomies 21, 18 and 13, but also has the potential for detecting chromosomal microdeletion/microduplications. For high risk fetuses indicated by NIPT, prenatal diagnosis needs to be carry out to verify the chromosomal abnormalities.

Case report: Molecular analysis of a 47,XY,+21/46,XX chimera using SNP microarray and review of literature

Chimerism is a very rare genetic finding in human. Most reported cases have a chi 46,XX/46,XY karyotype. Only three non-twin cases carrying both trisomy 21 and a normal karyotype have been reported, including two cases with a chi 47,XY,+21/46,XX karyotype and a case with a chi 47,XX,+21/46,XY karyotype. Herein we describe an additional case with a chi 47,XY,+21/46,XX karyotype. For the case, a physical examination at the age of 1year revealed ambiguous genitalia with no features of Down syndrome or other malformations. Growth and developmental milestones were within normal ranges. We performed short tandem repeat (STR) and single nucleotide polymorphism (SNP) microarray analyses to attempt to identify the mechanism underlying the chimerism in this patient and the origin of the extra chromosome 21. Cytogenetic analyses of the patient's peripheral blood revealed approximately 17% of a 47,XY,+21 lineage by G-banding karyotype analysis, 13%-17% by FISH analyses of uncultured peripheral blood, and 10%-15% by SNP microarray analysis. Four years later, the percentage of trisomy 21 cells had decreased to approximately 6%. SNP microarray and STR analyses revealed a single maternal and double paternal genetic contribution to the patient for the majority of the markers, including the chromosome 21 markers. The extra chromosome 21 was paternally derived and meiosis I nondisjunction likely occurred during spermatogenesis. The mechanisms underlying chimera in our case was likely fertilization two spermatozoa, one with an ovum and the other with the second polar body.

KIF1A novel frameshift variant p.(Ser887Profs*64) exhibits clinical heterogeneity in a Pakistani family with hereditary sensory and autonomic neuropathy type IIC

Background: Hereditary sensory and autonomic neuropathies (HSANs) are rare heterogeneous group of neurological disorders caused by peripheral nerve deterioration. The HSANs sub-clinical classes have clinical and genetic overlap which often lead to misdiagnosis. In the present study a Pakistani family with five affected members suffering from severe neuropathy were genetically analyzed to identify the disease causative element in the family. Methods: Genome wide high-density single nucleotide polymorphism (SNP) microarray analysis was carried out followed by whole exome sequencing of the affected proband and another affected sibling. Shared homozygous regions in all severely affected members were identified through homozygosity mapping approach. Results: The largest homozygous region of 14.1 Mb shared by the five severely affected members of the family was identified on chromosome 2. Subsequent exome sequencing identified a novel single nucleotide deletion c.2658del; p.(Ser887Profs*64) in KIF1A. Segregation analysis revealed that this mutation was homozygous in all five affected individuals of the family with severe clinical manifestation, while members of the family that were heterozygous carriers shared abnormal skin features (scaly skin) only with the homozygous affected members. Conclusions: A novel frameshift mutation p.(Ser887Profs*64) in KIF1A is the potential cause of severe HSANIIC in a Pakistani family along with incomplete penetrance in mutation carriers. We demonstrate that using a combination of different techniques not only strengthens the gene finding approach but also helps in proper sub-clinical characterization along with identification of mutated alleles exhibiting incomplete penetrance leading to intrafamilial clinical variability in HSAN group of inherited diseases.

Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception.

Conventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, as well as microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. The use of OGM precludes the requirement for culturing (and related microbial contamination). However, a high percentage of MCC impedes a definitive diagnosis, which can be addressed by an additional pre-analytical quality control step that includes histological assessment of H&E stained slides from formalin-fixed paraffin embedded (FFPE) tissue with macro-dissection for chorionic villi to enrich fetal tissue component for single nucleotide polymorphism microarray (SNPM) analysis. To improve the diagnostic yield, an integrated workflow was devised that included MCC characterization of POC tissue, followed by OGM for MCC-negative cases or SNPM with histological assessment for MCC-positive cases. A result was obtained in 93% (29/31) of cases with a diagnostic yield of 45.1% (14/31) with the proposed workflow, compared to 9.6% (3/31) and 6.4% (2/31) with routine workflow, respectively. The integrated workflow with these technologies demonstrates the clinical utility and higher diagnostic yield in evaluating POC specimens.

Characterization of a rare mosaic unbalanced translocation of t(3;12) in a patient with neurodevelopmental disorders

BackgroundUnbalanced translocations may be de novo or inherited from one parent carrying the balanced form and are usually present in all cells. Mosaic unbalanced translocations are extremely rare with a highly variable phenotype depending on the tissue distribution and level of mosaicism. Mosaicism for structural chromosomal abnormalities is clinically challenging for diagnosis and counseling due to the limitation of technical platforms and complex mechanisms, respectively. Here we report a case with a tremendously rare maternally-derived mosaic unbalanced translocation of t(3;12), and we illustrate the unreported complicated mechanism using single nucleotide polymorphism (SNP) array, fluorescence in situ hybridization (FISH), and chromosome analyses.Case presentationAn 18-year-old female with a history of microcephaly, pervasive developmental disorder, intellectual disability, sensory integration disorder, gastroparesis, and hypotonia presented to our genetics clinic. She had negative karyotype by parental report but no other genetic testing performed previously. SNP microarray analysis revealed a complex genotype including 8.4 Mb terminal mosaic duplication on chromosome 3 (3p26.3->3p26.1) with the distal 5.7 Mb involving two parental haplotypes and the proximal 2.7 Mb involving three parental haplotypes, and a 6.1 Mb terminal mosaic deletion on chromosome 12 (12p13.33->12p13.31) with no evidence for a second haplotype. Adjacent to the mosaic deletion is an interstitial mosaic copy-neutral region of homozygosity (1.9 Mb, 12p13.31). The mother of this individual was confirmed by chromosome analysis and FISH that she carries a balanced translocation, t(3;12)(p26.1;p13.31).ConclusionTaken together, the proband, when at the stage of a zygote, likely carried the derivative chromosome 12 from this translocation, and a postzygotic mitotic recombination event occurred between the normal paternal chromosome 12 and maternal derivative chromosome 12 to “correct” the partial 3p trisomy and partial deletion of 12p. To the best of our knowledge, it is the first time to report the mechanism utilizing a combined cytogenetic and cytogenomic approach, and we believe it expands our knowledge of mosaic structural chromosomal disorders and provides new insight into clinical management and genetic counseling.

Diagnosis of Chromosome 15q-Terminal Deletion Syndrome through Elevated Fasting Serum Growth Hormone Levels

Chromosome 15q26-qter deletion syndrome is a rare disease that causes prenatal and postnatal growth retardation, microcephaly, developmental delay, and congenital heart diseases, mainly due to haploinsufficiency of IGF1R. In addition, patients with pathogenic variants of the IGF1R show similar symptoms. We report the case of a 5-month-old girl with prenatal and postnatal growth retardation, microcephaly, and congenital heart disease. At 5 months of age, her length was 54.7 cm (−4.3 SD), her weight was 4.4 kg (−3.1 SD), and her head circumference was 37.4 cm (−2.8 SD), thus presenting severe growth retardation. Repeated pre-feeding serum GH levels were abnormally high (26.1–85.5 ng/mL), and IGF-1 levels (+0.16 to +1.2 SD) were relatively high. The 15q sub-telomere fluorescence in situ hybridization analysis revealed a heterozygous deletion in the 15q terminal region. Whole-genome single nucleotide polymorphism microarray analysis showed a terminal deletion of 6.4 Mb on 15q26.2q26.3. This is the first report showing that fasting GH levels are high in early infancy in patients with IGF1R abnormalities. In addition to relatively high IGF-1 levels, elevated fasting GH levels in early infancy may contribute to the diagnosis of IGF1R abnormalities.

Impact of SNP microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy

Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, an approach referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while DNA typically obtainable from crime scene stains is of low DNA quantity and quality, and SNP microarray data obtained from compromised DNA are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of compromised DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 ng to 6.25 pg led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 pg for siblings and 1st cousins, 1 ng for 2nd cousins, while at 25 pg and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800 to 200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones.

Genetic testing and prenatal diagnosis for a family with 10q22.3q23.2 microdeletion

To carry out genetic testing for a pregnant woman with mild mental retardation, facial dysmorphism, and a history of adverse pregnancies and provide prenatal diagnosis for her. Routine G-banded karyotyping and single nucleotide polymorphism microarray (SNP-array) analysis were performed on the couple and amniotic fluid sample. No karyotypic abnormality was found with the couple and amniotic fluid sample. SNP-array analysis showed that the woman has carried a 7.801 Mb microdeletion in 10q22.3q23.2, which involved 18 OMIM genes including CDHR1, BMPR1A, NRG3, GRID1 and LDB3, which are associated with facial abnormalities, developmental retardation, mental retardation and autism. The fetus also carried a 7.819 Mb deletion in the same region, while the father showed no abnormality. Both the pregnant woman and her fetus have carried a 10q22.3q23.2 microdeletion, which has provided guidance for her subsequent pregnancy.

Microarray Findings of Intraplacental Choriocarcinoma: A Report of Four Cases

Abstract Introduction/Objective Gestational trophoblastic neoplasia (GTN) is a group of poorly understood diseases characterized by an abnormal and overtly malignant proliferation of trophoblastic tissue. Choriocarcinoma, which may also be nongestational in origin, is a particularly invasive and aggressive variant of GTN that is composed of a dimorphic trophoblast population. Many studies have attempted to define choriocarcinoma via various cytogenetic, molecular, and epigenetic means; however, the exact etiology and pathogenesis of this tumor remain unclear, in large part due to its rarity. Estimates of the incidence of choriocarcinoma range from 1 in 24,000 to 1 in 40,000 pregnancies. Intraplacental tumors are even less common with 62 reported cases and an estimated incidence of 1 in 160,000 placentas. In an effort to better understand the pathogenesis of this rare entity, four cases of choriocarcinoma (of which three are intraplacental and one is intrauterine occurring one year following an unremarkable pregnancy) diagnosed at our institution since 2010 were identified for chromosomal microarray. Methods DNA was extracted from formalin-fixed, paraffin-embedded blocks of four matched cases: tumor and normal placenta. Single nucleotide polymorphism (SNP) microarray analysis was performed to assess genomic copy number differences between the tumor and the placenta from which it arose (Infinium Global Diversity Array-8 v1.0 BeadChip with an I Scan System; Illumina, San Diego, CA). Analysis of a placenta not affected by tumor was also performed. Results Early partial data review demonstrates copy number aberrations in choriocarcinoma arising in placental tissue. Additional interpretation of the data is ongoing. Conclusion DNA chromosomal microarray analysis was performed to search for genomic copy number differences in between the tumor and the placenta from which it arose. Recent studies suggest gestational choriocarcinoma oncogenesis may differ from that of other malignancies, but this conclusion is based on a low number of recurrent DNA mutations. SNP microarray analysis may further refine the current understanding of the oncogenesis of gestational choriocarcinoma.

The genetic cause of intellectual deficiency and/or congenital malformations in two parental reciprocal translocation carriers and implications for assisted reproduction.

To elucidate the genetic cause of intellectual deficiency and/or congenital malformations in two parental reciprocal translocation carriers and provide appropriate strategies of assisted reproductive therapy (ART). Two similar couples having a child with global developmental delay/intellectual disability symptoms attended the Reproductive and Genetic Hospital of CITIC-Xiangya (Changsha, China) in 2017 and 2019, respectively, in order to determine the cause(s) of the conditions affecting their child and to seek ART to have a healthy baby. Both of the healthy couples were not of consanguineous marriage, denied exposure to toxicants, and had no adverse life history. This study was approved by the Institutional Ethics Committee of the Reproductive & Genetic Hospital of CITIC-Xiangya, and written informed consent was obtained from the parents. Genetic diagnoses were performed by karyotype analysis, breakpoint mapping analysis of chromosomal translocation(s), single-nucleotide polymorphism (SNP) microarray analysis, and whole-exome sequencing (WES) for the two children and different appropriate reproductive strategies were performed in the two families. Karyotype analysis revealed that both patients carried parental reciprocal translocations [46,XY,t(7;16)(p13;q24)pat and 46,XY,t(13;17)(q12.3;p11.2)pat, respectively]. Follow-up breakpoint mapping analysis showed no interruption of associated genes, and SNP microarray analysis identified no significant copy number variations (CNVs) in the two patients. Moreover, WES results revealed that patients 1 and 2 harbored candidate compound heterozygous mutations of MCOLN1 [c.195G>C (p.K65N) and c.1061G>A (p.W354*)] and MCPH1 [c.877A>G (p.S293G) and c.1869_1870delAT (p.C624*)], respectively, that were inherited from their parents and not previously reported. Furthermore, the parents of patient 1 obtained 10 embryos during ART cycle, and an embryo of normal karyotype and non-carrier of observed MCOLN1 mutations according to preimplantation genetic testing for structural rearrangement and monogenic defect was successfully transferred, resulting in the birth of a healthy boy. The parents of patient 2 chose to undergo ART with donor sperm to reduce the risk of recurrence. Systematic genetic diagnosis of two carriers of inherited chromosomal translocations accompanied by clinical phenotypes revealed their cause of disease, which was critical for genetic counseling and further ART for these families.

Home collection of products of conception: Can chromosomal analysis be obtained?

IntroductionThe majority of early pregnancy losses are due to chromosomal abnormalities, which can be evaluated by testing the products of conception (POCs). Traditionally, a dilation and curettage (D&C) is recommended to patients to obtain suitable tissue for analysis. This case series sought to determine whether patients with first-trimester pregnancy losses can successfully obtain analysis of POCs if they pass tissue with expectant management or misoprostol, rather than D&C. Materials and methodsThis is a retrospective cohort study of patients who desired analysis of POCs following an early pregnancy loss. The POCs were collected either at home by patients, or by providers following a D&C, and sent to an outside laboratory for single nucleotide polymorphism (SNP) microarray analysis. ResultsOf 50 identified patients, chromosomal analysis was successfully completed on: 22/34 (65%) of patients who passed pregnancy with misoprostol, 14/14 (100%) with D&C, and 1/2 (50%) with expectant management (x2, p = 0.03). Analysis was successful up to 9 days after tissue was collected, and 55 days after diagnosis of loss. ConclusionIn our study, D&C was the superior method to obtain POCs for chromosomal analysis following a miscarriage, but medical and expectant management still had clinically acceptable success rates as well. Although further study is indicated, this small case series suggests that patient counselling regarding miscarriage management and desired chromosomal analysis should continue to include misoprostol and expectant management as inferior but still appropriate alternatives to D&C.

6q25.1 (TAB2) microdeletion is a risk factor for hypoplastic left heart: a case report that expands the phenotype

IntroductionHypoplastic left heart syndrome (HLHS) is a rare but devastating congenital heart defect (CHD) accounting for 25% of all infant deaths due to a CHD. The etiology of HLHS remains elusive, but there is increasing evidence to support a genetic cause for HLHS; in particular, this syndrome is associated with abnormalities in genes involved in cardiac development. Consistent with the involvement of heritable genes in structural heart abnormalities, family members of HLHS patients have a higher incidence of both left- and right-sided valve abnormalities, including bicuspid aortic valve (BAV).Case presentationWe previously described (Am J Med Genet A 173:1848–1857, 2017) a 4-generation family with a 6q25.1 microdeletion encompassing TAB2, a gene known to play an important role in outflow tract and cardiac valve formation during embryonic development. Affected adult family members have short stature, dysmorphic facial features, and multiple valve dysplasia, including BAV. This follow-up report includes previously unpublished details of the cardiac phenotype of affected family members. It also describes a baby recently born into this family who was diagnosed prenatally with short long bones, intrauterine growth restriction (IUGR), and HLHS. He was the second family member to have HLHS; the first died several decades ago. Postnatal genetic testing confirmed the baby had inherited the familial TAB2 deletion.ConclusionsOur findings suggest TAB2 haploinsufficiency is a risk factor for HLHS and expands the phenotypic spectrum of this microdeletion syndrome. Chromosomal single nucleotide polymorphism (SNP) microarray analysis and molecular testing for a TAB2 loss of function variant should be considered for individuals with HLHS, particularly in those with additional non-cardiac findings such as IUGR, short stature, and/or dysmorphic facial features.

Acute myeloid leukemia with inv(16)(p13.1q22) and deletion of the 5\u2019MYH11/3\u2019CBFB gene fusion: a report of two cases and literature review

BackgroundAbnormalities of chromosome 16 are found in about 5–8% of acute myeloid leukemia (AML). The AML with inv(16)(p13.1q22) or t (16;16)(p13.1;q22) is associated with a high rate of complete remission (CR) and favorable overall survival (OS) when treated with high-dose Cytarabine. At the inversion breakpoints, deletion of 3’CBFB has been reported, but most of them were studied by chromosome and fluorescence in situ hybridization (FISH) analyses. The genomic characteristics of such deletions remain largely undefined, hindering further understanding of the clinical significance of the deletions.Case presentationWe report here two AML cases with inv(16) and deletion of the 5’MYH11/3’CBFB gene fusion, which were characterized by chromosome, FISH, and single nucleotide polymorphism (SNP) microarray analyses. Both cases have achieved CR for more than three years.ConclusionsDeletion of 3’CBFB in AML with inv(16) is also accompanied with deletion of 5’MYH11 in all the cases studied by SNP microarray, suggesting that 3’CBFB and 5’MYH11 were most likely deleted together as a fusion product of inv(16) instead of occurring separately. In concert with the findings of other published studies of similar patients, our study suggests that deletion of 5’MYH11/3’CBFB in AML with inv(16) may not have negative impact on the prognosis of the disease.

Near haploidization is a genomic hallmark which defines a molecular subgroup of giant cell glioblastoma.

BackgroundGiant cell glioblastoma (gcGBM) is a rare histologic subtype of glioblastoma characterized by numerous bizarre multinucleate giant cells and increased reticulin deposition. Compared with conventional isocitrate dehydrogenase (IDH)-wildtype glioblastomas, gcGBMs typically occur in younger patients and are generally associated with an improved prognosis. Although prior studies of gcGBMs have shown enrichment of genetic events, such as TP53 alterations, no defining aberrations have been identified. The aim of this study was to evaluate the genomic profile of gcGBMs to facilitate more accurate diagnosis and prognostication for this entity.MethodsThrough a multi-institutional collaborative effort, we characterized 10 gcGBMs by chromosome studies, single nucleotide polymorphism microarray analysis, and targeted next-generation sequencing. These tumors were subsequently compared to the genomic and epigenomic profile of glioblastomas described in The Cancer Genome Atlas (TCGA) dataset.ResultsOur analysis identified a specific pattern of genome-wide massive loss of heterozygosity (LOH) driven by near haploidization in a subset of glioblastomas with giant cell histology. We compared the genomic signature of these tumors against that of all glioblastomas in the TCGA dataset (n = 367) and confirmed that our cohort of gcGBMs demonstrated a significantly different genomic profile. Integrated genomic and histologic review of the TCGA cohort identified 3 additional gcGBMs with a near haploid genomic profile.ConclusionsMassive LOH driven by haploidization represents a defining molecular hallmark of a subtype of gcGBM. This unusual mechanism of tumorigenesis provides a diagnostic genomic hallmark to evaluate in future cases, may explain reported differences in survival, and suggests new therapeutic vulnerabilities.

The Efficiency of SNP-Based Microarrays in the Detection of Copy-Neutral Events at 15q11.2 and 11p15.5 Loci.

Prader-Willi, Angelman, Beckwith-Wiedemann, and Russell-Silver are imprinting syndromes. In this study, we aimed to compare the efficiency of single nucleotide polymorphism (SNP) microarray analysis with methylation-specific Multiplex ligation-dependent probe amplification (MS-MLPA) in the detection of uniparental disomy in these syndromes. The patient samples with regions of loss of heterozygosity (LOH), covering 15q11.2 and 11p15.5 critical loci, were analyzed with MS-MLPA to demonstrate the efficiency of SNP microarray in the detection of uniparental disomy (UPD). In a total of seven patients, LOH covering 15q11.2 and 11p15.5 critical loci was detected. Two (28.6%) of these seven patients showed aberrant methylation (suggesting UPD) in MS-MLPA. SNP microarray is a useful tool in the detection of LOH; however, it should be used with caution, since false-positive or false-negative LOH results can be obtained. Although methylation analysis is recommended as the first tier test in the diagnosis of most of the imprinting disorders, combining methylation analysis with SNP microarray can enhance our evaluation process.

Abstract 844: Integrated analysis of genetic and epigenetic alterations in gastric carcinomas

Abstract Gastric carcinomas (GCs) have highly heterogeneous features in terms of clinical phenotypes, histological characters and molecular mechanisms. In our previous study based on Infinium HumanMethylation27 BeadChip, unsupervised hierarchical clustering analysis using genome-wide DNA methylation profiles of non-tumorous gastric mucosa (N) samples, being at the precancerous condition of GC, divided 110 GC patients into 3 subclusters. This epigenomic clustering based on DNA methylation profiles of N samples showed significant correlations with clinicopathological features of the corresponding carcinomas: For example, GCs belonging to Cluster B1 showed poorer differentiated histology, tumor aggressiveness and poorer outcome. To gain a further understanding of gastric carcinogenesis, we performed integrative analysis of genomics and epigenomics. Whole exome sequencing and single-nucleotide polymorphism microarray analysis were performed in 66 paired samples of GC and the corresponding N from the same patients of the previous epigenomic study. The datasets were analyzed by MutSigCV and GISTIC2.0 pipelines and significant accumulations of single nucleotide variation, insertion, deletion and copy number variation were identified within each of the epigenomic subclusters. Then we performed a pathway enrichment analysis using the genes genetically and epigenetically altered in each subcluster. Somatic mutation of the TP53, SMAD4, or ARID1A genes, which had been well known to occur in GCs, appeared with the same frequencies in 3 subclusters. On the other hand, a certain gene which has rarely reported before was recurrently mutated in our cohort. Epigenetic Cluster B1 was characterized by a fewer copy number alterations, and particularly by amplifications of 17q12, 10p11.1 and 3q26.2, including the genomic region of oncogene ERBB2. In integrated pathway enrichment analysis, p53-related pathways were enriched in Cluster A, and epithelial-mesenchymal transition (EMT)-related pathways were enriched in this particular Cluster B1. Poorly differentiated histological phenotype, i.e. loss of cell polarity or epithelial cell adhesion, may be attributable to molecular signature relating to EMT in Cluster B1. These data indicate that genetic and epigenetic alterations cooperate on gastric carcinogenesis thus impact on tumor aggressiveness. The consistency of molecular characteristics and pathological phenotypes suggests the possibility that future malignant progression can be predicted based on genetic and epigenetic alterations even at early stage of gastric carcinogenesis. Citation Format: Menghan Yang, Eri Arai, Hiromi Sakamoto, Hirohiko Totsuka, Hirokazu Taniguchi, Hitoshi Katai, Teruhiko Yoshida, Yae Kanai. Integrated analysis of genetic and epigenetic alterations in gastric carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 844.

Live born monochorionic dizygotic twins after in vitro fertilization: a case report

This paper reported a pair of twin babies who were diagnosed as monochorionic (MC) twins (MC) in the first-trimester ultrasound scan after in vitro fertilization. Fluorescence in situ hybridization and chromosomal karyotype analysis of amniotic fluid that was randomly collected from one of the twins were performed in the second trimester, but no abnormality was detected. Chromosome karyotype analysis of peripheral blood of the twins at the age of two days and three years showed that both were chi 47,XY,+21/46,XX. And the single nucleotide polymorphism microarray analysis of oral mucosa cells of the twins at three years old showed that the boy was 47,XY,+21 and the girl was 46,XX. Therefore, we confirmed that they are MC dizygotic twins presenting with blood chimerism but no tissue chimerism. Simply the boy presented with facial features of Down syndrome. Key words: Twins, dizygotic; Fertilization in vitro; In situ hybridization, fluorescence; Karyotyping; Polymorphism, single nucleotide

Copy number variation of LINGO1 in familial dystonic tremor.

ObjectiveTo elucidate the genetic cause of a large 5 generation South Indian family with multiple individuals with predominantly an upper limb postural tremor and posturing in keeping with another form of tremor, namely, dystonic tremor.MethodsWhole-genome single nucleotide polymorphism (SNP) microarray analysis was undertaken to look for copy number variants in the affected individuals.ResultsWhole-genome SNP microarray studies identified a tandem duplicated genomic segment of chromosome 15q24 present in all affected family members. Whole-genome sequencing demonstrated that it comprised a ∼550-kb tandem duplication encompassing the entire LINGO1 gene.ConclusionsThe identification of a genomic duplication as the likely molecular cause of this condition, resulting in an additional LINGO1 gene copy in affected cases, adds further support for a causal role of this gene in tremor disorders and implicates increased expression levels of LINGO1 as a potential pathogenic mechanism.

Whole-Genome Single Nucleotide Polymorphism Microarray for Copy Number and Loss of Heterozygosity Analysis in Tumors.

The basis of cancer biology is built upon two fundamental processes that result in uncontrolled cell proliferation and tumor formation: loss of tumor suppressor gene function and gain of oncogene function. Somatic DNA copy number variants (CNVs), which generally range in size from kilobases to entire chromosomes, facilitate gains and losses of chromosomal material incorporating oncogenes and tumor suppressor genes, respectively. In fact, many cancer types are characterized by DNA copy number changes and relatively few single nucleotide mutations (Ciriello et al. Nat Genet 45:1127-1133, 2013). Currently, the optimal method to detect such somatic copy number changes across the cancer genome is whole-genome single nucleotide polymorphism (SNP) microarray analysis.