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Background: Microarrays are a well-established and widely adopted technology capable of interrogating hundreds of thousands of loci across the human genome. Combined with imputation to cover common variants not included in the chip design, they offer a cost-effective solution for large-scale genetic studies. Beyond research applications, this technology can be applied for testing pharmacogenomics, nutrigenetics, and complex disease risk prediction. However, establishing clinical reporting workflows requires a thorough evaluation of the assay's performance, which is achieved through validation studies. In this study, we performed pre-clinical validation of a genetic testing workflow based on the Illumina Global Screening Array for 25 pharmacogenomic-related genes. Methods: To evaluate the accuracy of our workflow, we conducted multiple preclinical validation studies. Here, we present the results of accuracy and precision assessments, involving a total of 73 cell lines. These assessments encompass reference materials from the Genome-In-A-Bottle (GIAB), the Genetic Testing Reference Material Coordination Program (GeT-RM) projects, as well as additional samples from the 1000 Genomes project (1KGP). We conducted an accuracy assessment of genotype calls for target loci in each indication against established truth sets. Results: In our per-sample analysis, we observed a mean analytical sensitivity of 99.39% and specificity 99.98%. We further assessed the accuracy of star-allele calls by relying on established diplotypes in the GeT-RM catalogue or calls made based on 1KGP genotyping. On average, we detected a diplotype concordance rate of 96.47% across 14 pharmacogenomic-related genes with star allele-calls. Lastly, we evaluated the reproducibility of our findings across replicates and observed 99.48% diplotype and 100% phenotype inter-run concordance. Conclusion: Our comprehensive validation study demonstrates the robustness and reliability of the developed workflow, supporting its readiness for further development for applied testing. [ABSTRACT FROM AUTHOR]

Background: Microarrays are a well-established and widely adopted technology capable of interrogating hundreds of thousands of loci across the human genome. Combined with imputation to cover common variants not included in the chip design, they offer a cost-effective solution for large-scale genetic studies. Beyond research applications, this technology can be applied for testing pharmacogenomics, nutrigenetics, and complex disease risk prediction. However, establishing clinical reporting workflows requires a thorough evaluation of the assay’s performance, which is achieved through validation studies. In this study, we performed pre-clinical validation of a genetic testing workflow based on the Illumina Global Screening Array for 25 pharmacogenomic-related genes.Methods: To evaluate the accuracy of our workflow, we conducted multiple pre-clinical validation studies. Here, we present the results of accuracy and precision assessments, involving a total of 73 cell lines. These assessments encompass reference materials from the Genome-In-A-Bottle (GIAB), the Genetic Testing Reference Material Coordination Program (GeT-RM) projects, as well as additional samples from the 1000 Genomes project (1KGP). We conducted an accuracy assessment of genotype calls for target loci in each indication against established truth sets.Results: In our per-sample analysis, we observed a mean analytical sensitivity of 99.39% and specificity 99.98%. We further assessed the accuracy of star-allele calls by relying on established diplotypes in the GeT-RM catalogue or calls made based on 1KGP genotyping. On average, we detected a diplotype concordance rate of 96.47% across 14 pharmacogenomic-related genes with star allele-calls. Lastly, we evaluated the reproducibility of our findings across replicates and observed 99.48% diplotype and 100% phenotype inter-run concordance.Conclusion: Our comprehensive validation study demonstrates the robustness and reliability of the developed workflow, supporting its readiness for further development for applied testing.

Abstract Background Unbalanced 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 presentation An 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). Conclusion Taken 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.

Abstract Background Double aneuploidy is common, especially in products of conception, frequently involving a combination of a sex chromosome and an acrocentric chromosome. Double autosomal trisomies are rare with only five cases reported. Double aneuploidy mosaicism involving two different cell lines is rarer with only three cases reported. Case presentation We report a fourth case of double aneuploidy mosaicism on a baby. Results of a 24-h preliminary chromosome analysis at birth showed a mosaic karyotype, 47,XX,+18[15]/47,XX,+21[8]/48,XX,+21,+mar[7]. Reflex testing to SNP microarray with the same sample collected at birth showed gain of a 77.9 Mb region on chromosome 18 and gain of a 32.5 Mb region on chromosome 21. Microarray did not show any other copy number variants indicating that the marker chromosome may not contain any euchromatic material. A repeat chromosome analysis at 1-year of age showed a mosaic karyotype, 47,XX,+18[76]/47,XX,+21[4] with loss of the marker cell line. Conclusion Based on our results, we propose that the mosaic double autosomal trisomy in our case was due to two independent non-disjunction events in a normal zygote very early during embryogenesis.

The use of SNP microarrays has gained distinguished attention in recent years and the identification of numerous SNPs has proven valuable for genetic evaluation and selection in farm animals. In the current study we compared several bovine populations from Romania and Switzerland at the level of SNPs. Romanian Brown (N=39) and Romanian Spotted (N=245) cattle were genotyped using the Axiom Bovine BovMDv3 SNP microarray. For the Swiss population, we acquired sequencing data from the NCBI SRA database for 80 individuals from three breeds: Brown Swiss (N=20), Original Braunvieh (N=20) and Simmental (N=40). Sequencing data were processed using the Bcbio-nextgen data analysis pipeline and variants were called based on the UMD3.1 reference genome. Common SNPs found from both microarray and sequencing data were retained and genotypes from all the Romanian and Swiss animals were pooled together, resulting in a combined dataset of 48,291 SNPs for 364 individuals. Pairwise comparisons were assessed on the five subpopulations according to Weir and Cockerham’s FST index. Small genetic differences (FST < 0.05) were found between the Romanian Brown and Swiss Brown Swiss subpopulations and between Romanian Spotted and Swiss Simmental subpopulations. For all the other pairwise comparisons, FST values were between 0.05 and 0.1, indicating a moderate level of genetic difference among the corresponding subpopulations. The results of fastSTRUCTURE indicated that the most likely number (K) of subpopulations from the pooled dataset was between 8 and 12. Bar plots for K = 5, 8 and 12 confirmed that Romanian Brown and Swiss Brown Swiss subpopulations were genetically similar. However, they also revealed a surprisingly high level of heterogeneity among the Romanian Spotted individuals. As such, future research is required to zoom in on the genetic make-up and explain the most likely sources of heterogeneity for the Romanian Spotted breed. Current results will facilitate a better understanding of genomic selection and its application for improved breeding programs in Romanian cattle breeds.

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 1 year 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.

Living with an undiagnosed medical condition places a tremendous burden on patients, their families, and their healthcare providers. The Undiagnosed Diseases Program (UDP) was established at the National Institutes of Health (NIH) in 2008 with the primary goals of providing a diagnosis for patients with mysterious conditions and advancing medical knowledge about rare and common diseases. The program reviews applications from referring clinicians for cases that are considered undiagnosed despite a thorough evaluation. Those that are accepted receive clinical evaluations involving deep phenotyping and genetic testing that includes exome and genomic sequencing. Selected candidate gene variants are evaluated by collaborators using functional assays. Since its inception, the UDP has received more than 4500 applications and has completed evaluations on nearly 1300 individuals. Here we present six cases that exemplify the discovery of novel disease mechanisms, the importance of deep phenotyping for rare diseases, and how genetic diagnoses have led to appropriate treatment. The creation of the Undiagnosed Diseases Network (UDN) in 2014 has substantially increased the number of patients evaluated and allowed for greater opportunities for data sharing. Expansion to the Undiagnosed Diseases Network International (UDNI) has the possibility to extend this reach even farther. Together, networks of undiagnosed diseases programs are powerful tools to advance our knowledge of pathophysiology, accelerate accurate diagnoses, and improve patient care for patients with rare conditions. [ABSTRACT FROM AUTHOR]

Pharmacogenetic (PGx) testing has not been well adopted in current clinical practice. The phenotypic distribution of clinically relevant pharmacogenes remains to be fully characterized in large population cohorts. In addition, no study has explored actionable PGx alleles in the East Asian population at a large scale. This study comprehensively analyzed 14 actionable pharmacogene diplotypes and phenotypes in 172,854 Taiwanese Han individuals by using their genotype data. Furthermore, we analyzed data from electronic medical records to investigate the effect of the actionable phenotypes on the individuals. The PGx phenotype frequencies were comparable between our cohort and the East Asian population. Overall, 99.9% of the individuals harbored at least one actionable PGx phenotype, and 29% of them have been prescribed a drug to which they may exhibit an atypical response. Our findings can facilitate the clinical application of PGx testing and the optimization of treatment and dosage individually. [ABSTRACT FROM AUTHOR]

Background: Unbalanced 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 presentation: An 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). Conclusion: Taken 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. [ABSTRACT FROM AUTHOR]

Background: Double aneuploidy is common, especially in products of conception, frequently involving a combination of a sex chromosome and an acrocentric chromosome. Double autosomal trisomies are rare with only five cases reported. Double aneuploidy mosaicism involving two different cell lines is rarer with only three cases reported. Case presentation: We report a fourth case of double aneuploidy mosaicism on a baby. Results of a 24-h preliminary chromosome analysis at birth showed a mosaic karyotype, 47,XX,+18[15]/47,XX,+21[8]/48,XX,+21,+mar[7]. Reflex testing to SNP microarray with the same sample collected at birth showed gain of a 77.9 Mb region on chromosome 18 and gain of a 32.5 Mb region on chromosome 21. Microarray did not show any other copy number variants indicating that the marker chromosome may not contain any euchromatic material. A repeat chromosome analysis at 1-year of age showed a mosaic karyotype, 47,XX,+18[76]/47,XX,+21[4] with loss of the marker cell line. Conclusion: Based on our results, we propose that the mosaic double autosomal trisomy in our case was due to two independent non-disjunction events in a normal zygote very early during embryogenesis. [ABSTRACT FROM AUTHOR]

There are no evidence‐based guidelines to inform genetic counseling for consanguineous couples and their offspring. This focused revision builds on the expert opinions from the original publication of "Genetic Counseling and Screening of Consanguineous Couples and Their Offspring," based on a review of literature published since 2002. [ABSTRACT FROM AUTHOR]

Abstract Background Abnormalities 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 presentation We 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. Conclusions Deletion 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.

Abstract Background Cri-du-chat syndrome (CdCS; OMIM#123450) is a classic contiguous gene syndrome caused by chromosome 5p terminal deletion (5p-), which characterized by a high-pitched cat-like cry, developmental delay, severe psychomotor, mental retardation, and dysmorphic features in infancy. Prenatal diagnosis of CdCS is difficult due to the non-specific ultrasound features. And reports using array analysis are rare. This study presented the first retrospective analysis of prenatal series of CdCS fetuses diagnosed by single nucleotide polymorphism (SNP) array in China. Case presentation A total of 35,233 pregnant women were enrolled from Jan 2014 to April 2019 in our center, there are twelve 5p- cases with abnormal sonographic signs revealed by SNP array, giving an incidence of 0.034% (12/35,233). Clinical information and molecular basis included: maternal demographics, indications for invasive testing, sonographic findings and SNP array results. Among all the 5p- cases revealed, nine cases were diagnosed by both karyotyping and SNP array, three cases were detected only by SNP array. Half of our cases (6/12) had an isolated 5p terminal deletion, which sizes ranged from 9.0 Mb to 30 Mb. The other half of cases (6/12) characterized by unbalanced translocation, with sex ratio 7:5 (female: male), when combine the clinical features observed from this study and available literature, the most frequent anomaly observed in prenatal ultrasound examination of CdCS was cerebral abnormalities, accounted for 44.4% (16/36) of the existing cases. Features that are less consistent included: choroid plexus cyst (13.8%, 5/36), single umbilical artery (13.3%, 4/30), ventricular septal defect (11.1%, 4/36), hydrops fetalis (8.3%, 3/36), ascites (8.3%, 3/36), increased NT/NF (8.3%, 3/36), absent/severely hypoplastic nasal bone (5.5%, 2/36), in order. Conclusion Prenatal findings such as cerebral abnormalities, absent/hypoplastic nasal bone, hydrops fetalis, ascites or encephalocele may act as suggestive signs of CdCS or other microdeletion/duplication syndromes. Combining typical karyotyping with chromosomal microarray analysis (CMA) is a definitive method for a precise diagnosis of CdCS and provides more accurate results in order to offer genetic counseling to families which need to deal with cryptic aberrations.

Trisomy 12 is a rare autosomal aneuploidy. All postnatally diagnosed individuals with trisomy 12 have been mosaic for this chromosome abnormality. We herein report an infant girl presented at 2 weeks of age with severe congenital heart defect, tracheobronchomalacia, and dysmorphic features. All of the dysmorphic features of this patient fit into the known phenotype spectrum of mosaic trisomy 12, although this patient uniquely presented with macrocephaly. Tracheo‐bronchomalacia has been described once previously but had a significant impact on this patient's clinical course. The patient passed away at 2‐month‐old due to cardiac and respiratory complications. Chromosomal single nucleotide polymorphism (SNP) microarray analysis on a peripheral blood sample from the patient revealed trisomy 12 in approximately 50% of cells. Concurrent fluorescence in situ hybridization analysis of uncultured blood cells detected a comparable level of trisomy 12 mosaicism. Compared to conventional cytogenetics, SNP microarray examines all nucleated cells without sampling bias, has an increased power to estimate mosaicism level, and can provide a quick assessment of the underlying mechanism. Here we demonstrate the utilization of SNP microarray in the clinical diagnosis of those once considered rare disorders but might have been missed by conventional cytogenetic techniques. [ABSTRACT FROM AUTHOR]

We describe a patient with Temple syndrome resulting from maternal uniparental disomy of chromosome 14 who also has low‐level mosaicism for trisomy 14. UPD was initially suspected when SNP microarray analysis detected a large region of homozygosity on chromosome 14 and the patient's clinical features were consistent with the phenotype of upd(14)mat. However, SNP arrays cannot prove UPD, as homozygosity may also result from identity by descent. Methylation assays diagnose imprinting disorders such as Prader–Willi, Angelman and Temple syndromes; they detect methylation defects that occur in imprinted loci, which have parent‐of‐origin‐specific expression and have the advantage of making a diagnosis without parental samples. However, in this patient methylation analysis using endpoint PCR detected biparental inheritance. Therefore, sequencing analysis was performed and diagnosed upd(14)mat. Re‐examination of the microarray suggested that the explanation for the discrepancy between the array and methylation testing was low‐level mosaicism for trisomy 14 and fluorescence in situ hybridization testing detected a trisomic cell line. Thus, this patient's Temple syndrome is a result of a maternal M1 error, which gave a trisomic zygote, followed by loss of the paternal chromosome 14 in an early mitotic division to give maternal UPD with low‐level mosaicism for trisomy 14. The methylation assay detected the paternal allele in the trisomic line. The diagnostic failure of the methylation assay in this patient highlights a significant shortcoming of methylation endpoint analysis, especially for Temple syndrome, and underscores the need to use other methods in cases with mosaicism. [ABSTRACT FROM AUTHOR]

Deletion on the short arm of chromosome 18 is a rare disorder characterized by intellectual disability, growth retardation, and craniofacial malformations (such as prominent ears, microcephaly, ptosis, and a round face). The phenotypic spectrum is wide, encompassing a range of abnormalities from minor congenital malformations to holoprosencephaly. We present a case of a 2-year-old girl with ptosis, a round face, broad neck with low posterior hairline, short stature, and panhypopituitarism. She underwent ventilation tube insertion for recurrent otitis media with effusion. Brain magnetic resonance imaging showed an ectopic posterior pituitary gland and a shallow, small sella turcica with poor visualization of the pituitary stalk. Cytogenetic and chromosomal microarray analysis revealed a de novo deletion on the short arm of chromosome 18 (arr 18p11.32p11.21[136,227–15,099,116]x1). She has been treated with recombinant human growth hormone (GH) therapy since the age of 6 months after diagnosis of GH deficiency. Her growth rate has improved without any side effects from the GH treatment. This case expands the phenotypic spectrum of 18p deletion syndrome and emphasizes the positive impact of GH therapy on linear growth in this syndrome characterized by growth deficiency. Further studies are required to define the genotype-phenotype correlation according to size and loci of the deletion in 18p deletion syndrome and to predict prognosis.

A downside of next-generation sequencing technology is the high technical error rate. We built a tool, which uses array-based genotype information to classify next-generation sequencing–based SNPs into the correct and the incorrect calls. The deep learning algorithms were implemented via Keras. Several algorithms were tested: (i) the basic, naïve algorithm, (ii) the naïve algorithm modified by pre-imposing different weights on incorrect and correct SNP class in calculating the loss metric and (iii)–(v) the naïve algorithm modified by random re-sampling (with replacement) of the incorrect SNPs to match 30%/60%/100% of the number of correct SNPs. The training data set was composed of data from three bulls and consisted of 2,227,995 correct (97.94%) and 46,920 incorrect SNPs, while the validation data set consisted of data from one bull with 749,506 correct (98.05%) and 14,908 incorrect SNPs. The results showed that for a rare event classification problem, like incorrect SNP detection in NGS data, the most parsimonious naïve model and a model with the weighting of SNP classes provided the best results for the classification of the validation data set. Both classified 19% of truly incorrect SNPs as incorrect and 99% of truly correct SNPs as correct and resulted in the F1 score of 0.21 — the highest among the compared algorithms. We conclude the basic models were less adapted to the specificity of a training data set and thus resulted in better classification of the independent, validation data set, than the other tested models. [ABSTRACT FROM AUTHOR]

Acute myeloid leukemia (AML) in the setting of Noonan syndrome (NS) has been reported before without clear guidelines for treatment or prognosis in these subgroups of patients, most likely due to its rarity and incomplete understanding of the pathogenesis of both diseases. In the current era of next-generation sequencing-based genomic analysis, we can better identify patients with NS with more accurate AML-related prognostic markers. Germline mutations in PTPN11 are the most common cause of NS. Somatic mutations in NPM1 occur frequently in AML. Here, we describe a young adult patient with a novel combined germline PTPN11 and somatic NPM1, IDH1,and BCL6 mutations who presented with fatal AML. In addition, a 50.5-Mb interstitial deletion of 7q21.11-q33 in tumor DNA was detected by chromosomal microarray analysis. While mutations in the transcriptional repressor BCL6 are known to contribute to the pathogenesis of diffuse large B cell lymphoma (DLBCL) and chronic lymphocytic leukemia (CLL), its novel identification in this patient suggests an expanded role in aggressive AML. The identification of key molecular aberrations including the overexpression of SHP2, which drives leukemogenesis and tumorigenesis, has led to the development of novel investigational targeted SHP2 inhibitors. [ABSTRACT FROM AUTHOR]

Background: Genetic tests for primary immunodeficiency disorders (PIDs) are expensive, time-consuming, and not easily accessible in developing countries. Therefore, we studied the feasibility of a customized single nucleotide variant (SNV) microarray that we developed to detect disease-causing variants and copy number variation (CNV) in patients with PIDs for only 40 Euros.Methods: Probes were custom-designed to genotype 9,415 variants of 277 PID-related genes, and were added to the genome-wide Illumina Global Screening Array (GSA). Data analysis of GSA was performed using Illumina GenomeStudio 2.0, Biodiscovery Nexus 10.0, and R-3.4.4 software. Validation of genotype calling was performed by comparing the GSA with whole-genome sequencing (WGS) data of 56 non-PID controls. DNA samples of 95 clinically diagnosed PID patients, of which 60 patients (63%) had a genetically established diagnosis (by Next-Generation Sequencing (NGS) PID panels or Sanger sequencing), were analyzed to test the performance of the GSA. The additional SNVs detected by GSA were validated by Sanger sequencing.Results: Genotype calling of the customized array had an accuracy rate of 99.7%. The sensitivity for detecting rare PID variants was high (87%). The single sample replication in two runs was high (94.9%). The customized GSA was able to generate a genetic diagnosis in 37 out of 95 patients (39%). These 37 patients included 29 patients in whom the genetic variants were confirmed by conventional methods (26 patients by SNV and 3 by CNV analysis), while in 8 patients a new genetic diagnosis was established (6 patients by SNV and 2 patients suspected for leukemia by CNV analysis). Twenty-eight patients could not be detected due to the limited coverage of the custom probes. However, the diagnostic yield can potentially be increased when newly updated variants are added.Conclusion: Our robust customized GSA seems to be a promising first-line rapid screening tool for PIDs at an affordable price, which opens opportunities for low-cost genetic testing in developing countries. The technique is scalable, allows numerous new genetic variants to be added, and offers the potential for genetic testing not only in PIDs, but also in many other genetic diseases.

Dyggve melchior clausen syndrome (DMC, MIM 223800) is a very rare autosomal recessive form of skeletal dysplasia associated with various degrees of mental retardation. It is characterized by a progressive spondyloepimetaphyseal dysplasia (SEMD) with disproportionate short stature, generalized platyspondyly and lacy iliac crest. Here, we report characterization of large consanguineous family segregating DMC in autosomal recessive manner. Scanning SNP-based human genome identified a 5.3 Mb homozygous region on chromosome 18q21.1-q21.2. Sanger sequencing of the DYM gene, located in the homozygous region, revealed a novel homozygous nonsense variant [c.59 T > A; p.(Leu20*)] in affected members of the family. Analysis of the mRNA, extracted from hair follicles of an affected individual, suggested non-sense mediated decay (NMD) of the truncated transcript. This is the first nonsense and fourth loss of function variant in the DYM gene, causing DMC, reported in the Pakistani population. This study not only extended spectrum of the mutations in the DYM gene but will also facilitate diagnosis of similar other cases in Pakistani population. [ABSTRACT FROM AUTHOR]

The use of SNP microarrays has gained distinguished attention in recent years and the identification of numerous SNPs has proven valuable for genetic evaluation and selection in farm animals. In the current study we compared several bovine populations from Romania and Switzerland at the level of SNPs. Romanian Brown (N=39) and Romanian Spotted (N=245) cattle were genotyped using the Axiom Bovine BovMDv3 SNP microarray. For the Swiss population, we acquired sequencing data from the NCBI SRA database for 80 individuals from three breeds: Brown Swiss (N=20), Original Braunvieh (N=20) and Simmental (N=40). Sequencing data were processed using the Bcbio-nextgen data analysis pipeline and variants were called based on the UMD3.1 reference genome. Common SNPs found from both microarray and sequencing data were retained and genotypes from all the Romanian and Swiss animals were pooled together, resulting in a combined dataset of 48,291 SNPs for 364 individuals. Pairwise comparisons were assessed on the five subpopulations according to Weir and Cockerham's FST index. Small genetic differences (FST < 0.05) were found between the Romanian Brown and Swiss Brown Swiss subpopulations and between Romanian Spotted and Swiss Simmental subpopulations. For all the other pairwise comparisons, FST values were between 0.05 and 0.1, indicating a moderate level of genetic difference among the corresponding subpopulations. The results of fastSTRUCTURE indicated that the most likely number (K) of subpopulations from the pooled dataset was between 8 and 12. Bar plots for K = 5, 8 and 12 confirmed that Romanian Brown and Swiss Brown Swiss subpopulations were genetically similar. However, they also revealed a surprisingly high level of heterogeneity among the Romanian Spotted individuals. As such, future research is required to zoom in on the genetic make-up and explain the most likely sources of heterogeneity for the Romanian Spotted breed. Current results will facilitate a better understanding of genomic selection and its application for improved breeding programs in Romanian cattle breeds. [ABSTRACT FROM AUTHOR]

Background: Genetic tests for primary immunodeficiency disorders (PIDs) are expensive, time-consuming, and not easily accessible in developing countries. Therefore, we studied the feasibility of a customized single nucleotide variant (SNV) microarray that we developed to detect disease-causing variants and copy number variation (CNV) in patients with PIDs for only 40 Euros. Methods: Probes were custom-designed to genotype 9,415 variants of 277 PID-related genes, and were added to the genome-wide Illumina Global Screening Array (GSA). Data analysis of GSA was performed using Illumina GenomeStudio 2.0, Biodiscovery Nexus 10.0, and R-3.4.4 software. Validation of genotype calling was performed by comparing the GSA with whole-genome sequencing (WGS) data of 56 non-PID controls. DNA samples of 95 clinically diagnosed PID patients, of which 60 patients (63%) had a genetically established diagnosis (by Next-Generation Sequencing (NGS) PID panels or Sanger sequencing), were analyzed to test the performance of the GSA. The additional SNVs detected by GSA were validated by Sanger sequencing. Results: Genotype calling of the customized array had an accuracy rate of 99.7%. The sensitivity for detecting rare PID variants was high (87%). The single sample replication in two runs was high (94.9%). The customized GSA was able to generate a genetic diagnosis in 37 out of 95 patients (39%). These 37 patients included 29 patients in whom the genetic variants were confirmed by conventional methods (26 patients by SNV and 3 by CNV analysis), while in 8 patients a new genetic diagnosis was established (6 patients by SNV and 2 patients suspected for leukemia by CNV analysis). Twenty-eight patients could not be detected due to the limited coverage of the custom probes. However, the diagnostic yield can potentially be increased when newly updated variants are added. Conclusion: Our robust customized GSA seems to be a promising first-line rapid screening tool for PIDs at an affordable price, which opens opportunities for low-cost genetic testing in developing countries. The technique is scalable, allows numerous new genetic variants to be added, and offers the potential for genetic testing not only in PIDs, but also in many other genetic diseases. [ABSTRACT FROM AUTHOR]

We present 2 cases of double mosaic aneuploidy harboring 2 or more different aneuploid cell lines, but no line with a normal chromosome constitution. One of these cases presented mosaicism of sex chromosome aneuploid cell lines (47,XXX/45,X) along with another line containing an autosomal trisomy (47,XX,+8), while the other case showed mosaicism of 2 different autosomal trisomy cell lines (47,XY,+5 and 47,XY,+8). To elucidate the mechanisms underlying these mosaicisms, we conducted molecular cytogenetic analyses. Genotyping data from the SNP microarray indicated that 2 sequential meiotic or early postzygotic segregation errors likely had occurred followed by natural selection. These cases suggest that frequent segregation errors and selection events in the meiotic and early postzygotic stages lead to this condition. [ABSTRACT FROM AUTHOR]

Background: Abnormalities 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 presentation: We 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. Conclusions: Deletion 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. [ABSTRACT FROM AUTHOR]

Does advanced paternal age (APA; ≥40 years) contribute to a higher incidence of paternal origin aneuploidy in preimplantation embryos? This was a multicentre retrospective study of single-nucleotide polymorphism (SNP) microarray (Natera and Karyomapping) preimplantation genetic testing (PGT) outcomes of blastocyst-stage embryos. Whole-chromosome aneuploidy analysis was performed on 2409 embryos from 389 male patients undertaking 681 assisted reproductive technology (ART) cycles between 2012-2021. Segmental aneuploidy analysis was performed on 867 embryos from 140 men undertaking 242 ART cycles between 2016-2021. Embryos were grouped based on paternal age at sperm collection: <35, 35–39 and ≥40 years. Paternal and maternal origin aneuploidy rates were compared between groups using chi-squared and/or Fisher's exact tests. There was no significant difference across groups in paternal origin whole-chromosome aneuploidy rate, overall (P=0.7561) or when segregated by type (trisomy and monosomy: P=0.2235 and 0.8156) or complexity (single versus 2, 3 or ≥4 aneuploidies: P=0.9733, 0.7517, 0.669 and 0.1481). Conversely, maternal origin whole-chromosome aneuploidy rate differed across groups (P<0.0001) in alignment with differing mean maternal age (P<0.001). Paternal origin deletions were 2.9-fold higher than maternal origin deletions (P=0.0084), independent of age stratification. No significant difference in paternal origin deletions was observed with APA ≥40 compared with the younger age groups (4.8% versus 2.5% and 2.8%, P=0.5292). Individual chromosome aneuploidy rates were too low to perform statistical comparisons. No significant association was found between APA and the incidence of paternal origin aneuploidy in preimplantation embryos, irrespective of type or complexity. Thus, APA may not be an indication for PGT. [ABSTRACT FROM AUTHOR]

Deletion on the short arm of chromosome 18 is a rare disorder characterized by intellectual disability, growth retardation, and craniofacial malformations (such as prominent ears, microcephaly, ptosis, and a round face). The phenotypic spectrum is wide, encompassing a range of abnormalities from minor congenital malformations to holoprosencephaly. We present a case of a 2-year-old girl with ptosis, a round face, broad neck with low posterior hairline, short stature, and panhypopituitarism. She underwent ventilation tube insertion for recurrent otitis media with effusion. Brain magnetic resonance imaging showed an ectopic posterior pituitary gland and a shallow, small sella turcica with poor visualization of the pituitary stalk. Cytogenetic and chromosomal microarray analysis revealed a de novo deletion on the short arm of chromosome 18 (arr 18p11.32p11.21[136,227-15,099,116]x1). She has been treated with recombinant human growth hormone (GH) therapy since the age of 6 months after diagnosis of GH deficiency. Her growth rate has improved without any side effects from the GH treatment. This case expands the phenotypic spectrum of 18p deletion syndrome and emphasizes the positive impact of GH therapy on linear growth in this syndrome characterized by growth deficiency. Further studies are required to define the genotype-phenotype correlation according to size and loci of the deletion in 18p deletion syndrome and to predict prognosis. [ABSTRACT FROM AUTHOR]

Biparental/androgenetic mosaicism is a rarely diagnosed condition in humans. It is typically ascertained prenatally on the basis of placental mesenchymal dysplasia. Fetal outcome can range from demise due to intrauterine growth retardation to term delivery. Most of the published cases of liveborns represent females that are either completely normal or have features of Beckwith‐Wiedemann syndrome. Only two healthy liveborn males with mosaicism detected in the placenta have been described to date. Here, we report another liveborn male with hepatic mesenchymal hamartoma, soft tissue overgrowth on his right fifth toe, hemangiomas over his chest, right buttock and foot, anemia, thrombocytopenia and congenital hypothyroidism with biparental/androgenetic mosaicism detected in the toe mass in addition to the placenta. This new case adds to the existing literature of individuals with biparental/androgenetic mosaicism and expands the range of clinical presentations that may be seen in male patients with this condition. This study also illustrates the important use of single‐nucleotide polymorphism microarray in conjunction with short‐tandem repeat analysis on affected tissue to provide a diagnosis for patients with features of overgrowth and prior, non‐diagnostic, genetic analyses of their peripheral blood. [ABSTRACT FROM AUTHOR]

Interstitial deletions of chromosome 9q31 are very rare. The deletions in most reported patients have been detected by conventional cytogenetics, with reported breakpoints ranging between 9q21 and 9q34. Therefore, an accurate description of a "9q31 deletion syndrome" could not be established. However, based on microarray studies, a small region of overlap has recently been proposed. We report clinical features of two unrelated individuals with overlapping 9q deletions identified by SNP microarray analysis. Patient 1 has a 9 Mb deletion, while Patient 2's deletion was 21.6 Mb. The clinical features common to our patients and those in the literature include developmental delay and short stature. Patient 2 shows additional features not reported in other 9q31 deletions, such as hearing loss, ventriculomegaly, cleft lip and palate, and small kidneys, which could be due to the larger size of the deletion, hence the influence of the genes in the region beyond the smallest region of overlap. Based on the comparison of these patients with the previously reported patients, we redefine the smallest region of overlap and characterize the clinical features of the 9q31 deletion syndrome. [ABSTRACT FROM AUTHOR]

Yersinia pestis, the causative agent of plague, is a recently evolved clone of the enteropathogenic bacterium Yersinia pseudotuberculosis. Y. pestis has been extensively studied for decades; however, there are insufficient data about the intra-species diversity of this microorganism in certain parts of the world, including the Caucasus region. Using a high-density single-nucleotide polymorphism (SNP) microarray, we genotyped a total of 46 Y. pestis isolates from two plague foci in Georgia and neighboring Caucasus countries together with 12 Y. pseudotuberculosis isolates from Georgia. The genotyping microarray captured a total of 13,525 SNP positions across the Y. pestis and Y. pseudotuberculosis genomes and plasmids with high-throughput capability and superior reproducibility. From this analysis, we confirmed the presence of two independent and relatively distant phylogenetic groups of Y. pestis in the Caucasus region. The signature SNP patterns identified from this study will allow assay development for plague surveillance and pseudotuberculosis diagnostics. [ABSTRACT FROM AUTHOR]

Increasing clubroot resistance (CR) of Brassica oleracea by ascertaining the molecular mechanisms has been the key focus in modern B. oleracea breeding. In order to identify the quantitative trait loci (QTLs) associated with CR in B. oleracea, 94 F2 vegetative lines which were developed by tissue culture of selfed seeds from the F1 generation between a clubroot-resistant B. oleracea inbred line and a susceptible line, were identified for disease incidence and six CR-associated traits under a lab inoculation by Plasmodiophora brassicae and were genotyped with the 60K Brassica SNP array. Significant correlations were detected for numbers of fibrous roots and P. brassicae content in roots with disease incidence. Nine linkage groups were constructed from 565 bins which covered around 3,000 SNPs, spanning 1,028 cM of the B. oleracea genome with an average distance of 1.82 cM between adjacent bins. A total of 23 QTLs were identified for disease incidence and the other two correlated traits, individually explaining 6.1–17.8% of the phenotypic variation. Several overlaps were detected among traits, including one three-traits-overlapped locus on linkage group C08 and two important overlapped regions between the two CR-associated traits on C06. The QTLs were compared with known CR loci/genes and the novelty of our QTLs was discussed.

A complex mosaicism of the short arm of chromosome 1 detected by SNP microarray analysis is described in a patient presenting a 4-Mb 1p36 terminal deletion and associated phenotypic features. The array pattern of chromosome 1p displayed an intriguing increase in divergence of the SNP heterozygote frequency from the expected 50% from the centromere towards the 1p36 breakpoint. This suggests that various overlapping segments of UPD were derived by somatic recombination between the 1p homologues. The most likely explanation was the occurrence of a series of events initiated in either a gamete or an early embryonic cell division involving a 1pter deletion rapidly followed by multiple telomere captures, resulting in additive, stepped increases in frequency of homozygosity towards the telomere. The largest segment involved the entire 1p, and at least four other capture events were observed, indicating that at least five independent telomere captures occurred in separate cell lineages. The determination of breakpoint position by detection of abrupt changes in B-allele frequency using a moving window analysis demonstrated that they were identical in blood and saliva, the tissues available for analysis. We developed a model to explain the interaction of parameters determining the mosaic clones and concluded that, while number, size, and position of telomere captures were important initiating determinants, variation in individual clone frequencies was the main contributor to mosaic differences between tissues. All previous reports of telomere capture have been restricted to single events. Other cases involving multiple telomere capture probably exist but require investigation by SNP microarrays for their detection. [ABSTRACT FROM AUTHOR]

Interstitial deletions of the distal short arm of chromosome 2 including MYCN have only been reported for a small number of individuals. Germline deletions and mutations of MYCN cause Feingold syndrome 1 (FS1), a rare disorder characterized by microcephaly, digit anomalies, gastrointestinal atresias, short stature, dysmorphic features, and intellectual disability. We present a series of six individuals referred for SNP microarray with overlapping deletions of 2p ranging from 3.4 to 16.8 Mb in size, with a common overlapping region of 1.53 Mb spanning (14,614,477–16,148,021) [hg19] and including five genes: NBAS, DDX1, MYCNUT, MYCNOS, and MYCN. Clinical information was available for five individuals. Clinical features included core features of FS1 such as microcephaly, digit anomalies, and gastrointestinal atresias as well as structural cardiac defects, hearing loss, and renal anomalies, which are features less consistently associated with FS1. Other features observed in several individuals, that have not specifically been associated with FS1 were motor delay, structural brain abnormalities, genital abnormalities, and radioulnar synostosis. These results indicate that while individuals with deletions of 2p spanning several megabases and including MYCN can present with features not typically associated with FS1, the common core features are usually present. [ABSTRACT FROM AUTHOR]

Purpose While chromosomal regions of homozygosity (ROH) may implicate genes in known recessive disorders, their correlation to disease pathogenicity remains unclear. ROH around the centromere of the X chromosome (pericentromeric, pROH) is regarded as benign, although this has not been empirically demonstrated. Methods We examined microarray results from 122 female individuals harboring ROH bordering the X centromere. Results Consecutive ROH was most frequently observed for regions Xp11.23 to Xp11.21 and Xq11.1 to Xq12, with an average total size of 16.5 Mb. X chromosome pROH was unlikely related to phenotype in 41% (50/122) of cases due to other explanations: likely pathogenic deletion/duplication (17%, 21/122), apparently unaffected female (7%, 8/122), other clinical explanation (7%, 9/122), or consanguinity (10%, 12/122). Of the remaining cases with pROH as the only finding, four genes were associated with recessive disorders that overlapped one or more clinical features reported in our probands ( KDM5C , FGD1 , ZC4H2 , and LAS1L ). X chromosome pROH observed in our cohort overlapped with previously reported regions. Conclusions pROH on the X chromosome are commonly observed in both affected individuals with alternate causes of disease as well as in unaffected individuals, suggesting that X chromosome pROH has no clinically significant effect on phenotype. [ABSTRACT FROM AUTHOR]

Increasing clubroot resistance (CR) of Brassica oleracea by ascertaining the molecular mechanisms has been the key focus in modern B. oleracea breeding. In order to identify the quantitative trait loci (QTLs) associated with CR in B. oleracea, 94 F2 vegetative lines which were developed by tissue culture of selfed seeds from the F1 generation between a clubroot-resistant B. oleracea inbred line and a susceptible line, were identified for disease incidence and six CR-associated traits under a lab inoculation by Plasmodiophora brassicae and were genotyped with the 60K Brassica SNP array. Significant correlations were detected for numbers of fibrous roots and P. brassicae content in roots with disease incidence. Nine linkage groups were constructed from 565 bins which covered around 3,000 SNPs, spanning 1,028 cM of the B. oleracea genome with an average distance of 1.82 cM between adjacent bins. A total of 23 QTLs were identified for disease incidence and the other two correlated traits, individually explaining 6.1–17.8% of the phenotypic variation. Several overlaps were detected among traits, including one three-traits-overlapped locus on linkage group C08 and two important overlapped regions between the two CR-associated traits on C06. The QTLs were compared with known CR loci/genes and the novelty of our QTLs was discussed. [ABSTRACT FROM AUTHOR]

Background & Objective: Polycystic Ovary Syndrome (PCOS) is the major cause of infertility in females. PCOS is a complex and multifactorial disease, genetic and environmental factors being important predisposing factors. Diagnosis of PCOS is difficult due to the complexity of this disease; hence, better diagnostic tests are required to improve its management. Aim of the study was to elucidate the genetic causes of PCOS in three Pakistani families. Methods: Three Pakistani families segregating PCOS in an apparently autosomal recessive mode were recruited. Whole genome Single Nucleotide Polymorphism (SNP) genotyping and Whole Exome Sequencing (WES) were carried out to identify the candidate genes. Results: SNP genotypes data analyses identified multiple regions of homozygosity on different chromosomes. WES was performed in affected members of the family. Screening for pathogenic mutations in homozygous regions failed to detect any mutation/variant of interest. Conclusion: PCOS is multifactorial and complex disease so variants in the coding as well as in non-coding regions may be the genetic causes of the disease. To elucidate the genetic cause(s) of the PCOS, Whole Genome Sequencing (WGS) is recommended to cover both coding and non-coding regions of the genome. [ABSTRACT FROM AUTHOR]

Intellectual disability (ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In the last decade, microarray-based copy number variation (CNV) analysis has been proved as a strategy particularly useful in the discovery of loci and candidate genes associated with these phenotypes and is widely used in the clinics with a diagnostic purpose. In this study, we evaluated the usefulness of two genome-wide high density SNP microarrays -Cytogenetics Whole-Genome 2.7 M SNP array ( n = 126 patients; Group 1) and CytoScan High-Density SNP array ( n = 447 patients; Group 2)- in the detection of clinically relevant CNVs in a cohort of ID patients from Galicia (NW Spain). In 159 (27.7%) patients, we detected 186 rare exonic chromosomal imbalances, that were grouped into the following classes: Clinically relevant (67/186; 36.0%), of unknown clinical significance (93/186; 50.0%) and benign (26/186; 14.0%). The 67 pathogenic CNVs were identified in 64 patients, which means an overall diagnostic yield of 11.2%. Overall, we confirmed that ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide high density SNP microarrays in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with pathogenic or likely pathogenic CNVs and discussed the potential implication in neurodevelopmental disorders of genes located within these variants. [ABSTRACT FROM AUTHOR]

Maternal uniparental disomy (UPD) 15 is one of the molecular causes of Prader-Willi syndrome (PWS), a multisystem disorder which presents with neonatal hypotonia and feeding difficulty. Current diagnostic algorithms differ regarding the use of SNP microarray to detect PWS. We retrospectively examined the frequency with which SNP microarray could identify regions of homozygosity (ROH) in patients with PWS. We determined that 7/12 (58%) patients with previously confirmed PWS by methylation analysis and microsatellite- positive UPD studies had ROH (>10 Mb) by SNP microarray. Additional assessment of 5,000 clinical microarrays, performed from 2013 to present, determined that only a single case of ROH for chromosome 15 was not caused by an imprinting disorder or identity by descent. We observed that ROH for chromosome 15 is rarely incidental and strongly associated with hypotonic infants having features of PWS. Although UPD microsatellite studies remain essential to definitively establish the presence of UPD, SNP microarray has important utility in the timely diagnostic algorithm for PWS. [ABSTRACT FROM AUTHOR]

Testicular maturation arrest is characterized by interruption of germ cell development and differentiation. Genetic factors play important role in the causation of human disease, including male infertility. The objective was to study copy number variations in testicular maturation arrest using single nucleotide polymorphism ( SNP) microarray technique. Conventional cytogenetics, targeted fluorescence in situ hybridization ( FISH) and sequence-tagged site ( STS) polymerase chain reaction ( PCR) were used to confirm some of the SNP microarray findings. SNP microarray on 68 cases of testicular maturation arrest detected copy number variations ( CNVs) mostly on sex chromosomes involving pseudoautosomal regions ( PAR) 1, 2 and 3 as well as azoospermic factors ( AZFs) besides three cases of chromosomal abnormalities (two Klinefelter syndromes and one case of dicentric Y). The AZF deletion was observed in 14 (20.6%) cases and the AZFc gain was observed in 6 (8.8%) cases. PAR 1 and 2 CNVs was observed in 5 (7.3%) cases. PAR 3 CNVs was detected in 19 cases and 2 controls. The TSPY2 gene gain (within PAR 3 CNVs) was observed in 16 cases and 1 control. CNV containing autosomal genes possibly associated with male infertility in this study was SPATA31A2-A5 (9p12) in five cases. In this study, SNP microarray identified possible underlying aetiology in 55.9% (38/68) cases besides identifying minimal critical region of AZFc deletion as 0.51 mb (Y:24356128-24873665) involving TTY5, RBMY2FP, RBMY1F, RBMY1J, TTY6 and PRY genes. SNP microarray seems superior, sensitive, specific as well as cost-effective method and has potential to be the first tier investigations to explore underlying genomic factors of testicular maturation arrest. The present study is an attempt to find out probable genomic factors with idiopathic testicular maturation arrest. [ABSTRACT FROM AUTHOR]

Constitutional chromoanagenesis events, which include chromoanasynthesis and chromothripsis and result in highly complex rearrangements, have been reported for only a few individuals. While rare, these phenomena have likely been underestimated in a constitutional setting as technologies that can accurately detect such complexity are relatively new to the mature field of clinical cytogenetics. G-banding is not likely to accurately identify chromoanasynthesis or chromothripsis, since the banding patterns of chromosomes are likely to be misidentified or oversimplified due to a much lower resolution. We describe a patient who was initially referred for cytogenetic testing as a child for speech delay. As a young adult, he was referred again for recurrent strokes. Chromosome analysis was performed, and the rearrangement resembled a simple duplication of 13q32q34. However, SNP microarray analysis showed a complex pattern of copy number gains and a loss consistent with chromo-anasynthesis involving distal 13q (13q32.1q34). This report emphasizes the value of performing microarray analysis for individuals with abnormal or complex chromosome rearrangements. [ABSTRACT FROM AUTHOR]

Background: Intrachromosomal amplification of chromosome 21 (iAMP21) results from breakage-fusion-bridge cycles and chromothripsis is a distinct marker of a subgroup of B cell acute lymphoblastic leukemia (B-ALL) cases associated with a poor prognosis. iAMP21 accounts for 2% of pediatric B-ALL and occurs predominantly in older children or adolescents. ETV6-RUNX1 fusion, resulting from t(12;21)(p13;q22), is associated with an excellent outcome in younger children with B-ALL. Coexistence of iAMP21 with ETV6-RUNX1 fusion is extremely rare with limited clinical information available. Results: We report the case of an 18-year old Caucasian man diagnosed with ETV6-RUNX1 fusion positive B-ALL. He was treated with intensive chemotherapy and achieved remission for 6 months before relapse, 15 months after the initial diagnosis. G-band karyotyping and Fluorescence in situ hybridization (FISH) analyses performed on bone marrow revealed complex abnormalities: 41,X,-Y,der(3)t(3;20)(p11.2;q11.2),-4,t(5;22)(q32;q11.2),del(9)(p13),dic(9;17) (p13;p11.2),t(12;21)(p13;q22),der(14)t(14;17)(p11.2;q11.2),der(17;22)(q11.2;q11.2),-20,add(21)(q22),-22[4]/46,XY[15] with an iAMP21 and an ETV6-RUNX1. Additional molecular studies confirmed ETV6-RUNX1 fusion and with a TP53 mutation. High-resolution single nucleotide polymorphism microarray (SNP array) revealed the iAMP21 to be chromothripsis of 21q and subsequent metaphase FISH further delineated complex genomic aberrations. Although the patient received intensive chemotherapy with allogenic stem cell transplant, he died 26 months after initial diagnosis. We searched the literature and identified six cases showing coexisting iAMP21 and ETV6-RUNX1. The median age for these six patients was 10 years (range, 2-18) and males predominated. The median overall survival (OS) was 28 months. Conclusions: Patients with B-ALL associated with both iAMP21 and ETV6-RUNX1 tend to be older children or adolescents and have a poor prognosis. [ABSTRACT FROM AUTHOR]

Temple syndrome (TS, MIM 616222) is an imprinting disorder involving genes within the imprinted region of chromosome 14q32. TS is a genetically complex disorder, which is associated with maternal uniparental disomy of chromosome 14 (UPD14), paternal deletions on chromosome 14, or loss of methylation at the intergenic differentially methylated region (IG-DMR). Here, we describe the case of a patient with maternal hetero-UPD14, mixed iso-/hetero-disomy mechanism identified by a single nucleotide polymorphism (SNP) array analysis of patient-father duos study. The phenotype of our case is similarities to Prader-Willi syndrome (PWS) during infancy and to Russell-Silver syndrome (RSS) during childhood. This SNP array appears to be an effective initial screening tool for patients with nonspecific clinical features suggestive of chromosomal disorders. [ABSTRACT FROM AUTHOR]

Thefewproximal 4q chromosomal aberrations identified in patients with neurodevelopmental phenotypes that have been published to date are variable in type, size and breakpoints and, therefore, encompass different chromosome bands and genes, making the establishment of genotype-phenotype correlations a challenging task. Here, microarray-based copy number analysis allowed us the detection of two novel and partially overlapping deletions in two unrelated families. In Family 1, a 4q13.1-q13.2 deletion of 3.84Mb was identified in a mother with mild intellectual disability and in her two children, both with mild intellectual disability and attention deficit hyperactivity disorder. In Family 2, a de novo 4q13.2-q13.3 deletion of 6.81Mb was detected in a female patient, born to unaffected parents, with a diagnosis of mild intellectual disability, behavioral disorder and facialdysmorphism. The shortest region of overlap between these two aberrations is located at chromosome 4q13.2 and includes 17 genes amongst of which we suggest UBA6 (ubiquitin-like modifier-activating enzyme 6) as a strongcandidate gene for thesephenotypes. [ABSTRACT FROM AUTHOR]

Objectives: The histologic and immunohistochemical variability of renal epithelial tumors makes classification difficult; with significant clinical implications, efforts to make the proper diagnoses are necessary. Single-nucleotide polymorphism (SNP) microarray analysis has been proposed as a supplementary study for the classification of renal epithelial neoplasms; however, its practical use in the routine clinical setting has not been explored.Methods: Surgical pathology cases that were classified histologically as renal epithelial tumor subtypes and had concurrent SNP microarray were retrospectively reviewed to correlate tumor morphology and SNP microarray results.Results: Of the 99 cases reviewed, 88 (89%) had concordant histologic and microarray results. Four (4%) cases were unclassifiable by microarray due to uncharacteristic chromosomal abnormalities. Seven (7%) of the 99 cases had discordant microarray and histologic diagnoses, and following review of the histology, the diagnoses in two of these cases were subsequently changed.Conclusions: For most cases, concurrent SNP microarray confirmed the histologic diagnosis. However, discrepant microarray results prompted review of morphology and further ancillary studies, resulting in amendment of the final diagnosis in 29% of discrepant cases. SNP microarray analysis can be used to assist with the diagnosis of renal epithelial tumors, particularly those with atypical morphologic features. [ABSTRACT FROM AUTHOR]

DiGeorge syndrome (velocardiofacial syndrome, VCFS, 22q11DS) is caused by a microdeletion of approximately 40 genes from one copy of chromosome 22. Expression of the syndrome is a variable combination of more than 190 phenotypic characteristics, the most common are congenital heart disease, cleft palate and velopharyngeal insufficiency. Limb anomalies of hands and feets are not a typical clinical symptoms of DiGeorge syndrome. The aim of the study was to evaluate the extent of genomic changes in a 4.5 years old child with classical phenotypic features of 22q11DS in combination with severe ectrodactyly of all four limbs in addition; using microarray based single nucleotide polymorphism techniques in order to explain the origin of limb anomaly defects. FISH analysis, TP63 gene sequencing and whole genome SNP array analysis using HumanCytoSNP-12 DNA Analysis Beadchip (Illumina Inc.) were performed. FISH method revealed DiGeorge syndrome, TP63 gene sequencing did not detect any deleterious mutation, microarray SNP analysis established microdeletion of 22q11.2 region in standard defined range of 2,9 Mb. The original possible hypothesis, that in a patient it could exist a much more genomic changes than only these related to 22q11.2 region, involving genes associated with limb development and formation and thus explaining devastating limbs damage in patient, unfortunately was not confirmed. Although limb defects do not belong to the typical pathogenic signs of DiGeorge syndrome, this diagnosis should be considered in all neonate with congenital heart defect, cleft palate and limb anomalies. Even though variable phenotypical expressivity in DiGeorge syndrome is frequent, we can not exclude the possibility of coincidence of two independent genetic defects in our patient; DiGeorge syndrome due to 22q11.2 microdeletion and ectrodactyly which results of another gene/s mutation. [ABSTRACT FROM AUTHOR]

We describe the case of a male newborn with ring chromosome 13 found to have dysmorphic features, growth retardation, imperforate anus, and ambiguous genitalia. An initial karyotype showed 46,XY,r(13)(p13q34) in the 30 cells analyzed. SNP microarray from peripheral blood revealed not only an 8.14-Mb 13q33.2q34 deletion, but also a duplication of 87.49 Mb suggesting partial trisomy 13q that the patient did not appear to have clinically. Further cytogenetic characterization detected 3 distinct cell lines in the repeated peripheral blood sample: 46,XY,r(13)(p13q34)[89]/ 46,XY,r(13;13)(p13q34)[7]/45,XY,-13[5] and 2 in cultured fibroblasts: 46,XY,r(13)(p13q34)[65]/45,XY,-13[35]. Repeated molecular studies on peripheral blood and fibroblasts, however, failed to document the initially seen partial trisomy 13q. We postulate that the presence of duplicated material may be evidence of the high burden of duplicate rings in peripheral blood at any given time, with the high rates of cell death caused by mitotically unstable double rings accounting for the repeated microarray results that failed to detect any duplications. We emphasize the correlation between both cytogenetic and molecular studies with thorough clinical assessment and suggest that given the high sensitivity of newer molecular cytogenetic techniques, careful interpretation of results is critical in the context of ring chromosomes. © 2014 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]