Advances in identification methods of alien genomic components in plants / 生物工程学报

Plants with alien genomic components (alien chromosomes / chromosomal fragments / genes) are important materials for genomic research and crop improvement. To date, four strategies based on trait observation, chromosome analysis, specific proteins, and DNA sequences have been developed for the identification of alien genomic components. Among them, DNA sequence-based molecular markers are mainly used to identify alien genomic components. This review summarized several molecular markers for identification of alien genomic components in wheat, cabbage and other important crops. We also compared the characteristics of nine common molecular markers, such as simple sequence repeat (SSR), insertion-deletion (InDel) and single nucleotide polymorphism (SNP). In general, the accuracy of using a combination of different identification methods is higher than using a single identification method. We analyzed the application of different combination of identification methods, and provided the best combination for wheat, brassica and other crops. High-throughput detection can be easily achieved by using the new generation molecular markers such as InDel and SNP, which can be used to determine the precise localization of alien introgression genes. To increase the identification efficiency, other new identification methods, such as microarray comparative genomic hybridization (array-CGH) and suppression subtractive hybridization (SSH), may also be included.

Using Array-Based Comparative Genomic Hybridization to Diagnose Pallister-Killian Syndrome

Pallister-Killian syndrome (PKS) is a rare multisystem disorder characterized by isochromosome 12p and tissue-limited mosaic tetrasomy 12p. In this study, we diagnosed three pediatric patients who were suspicious of having PKS using array-based comparative genomic hybridization (array CGH) and FISH analyses performed on peripheral lymphocytes. Patients 1 and 2 presented with craniofacial dysmorphic features, hypotonia, and a developmental delay. Array CGH revealed two to three copies of 12p in patient 1 and three copies in patient 2. FISH analysis showed trisomy or tetrasomy 12p. Patient 3, who had clinical features comparable to those of patients 1 and 2, was diagnosed by using FISH analysis alone. Here, we report three patients with mosaic tetrasomy 12p. There have been only reported cases diagnosed by chromosome analysis and FISH analysis on skin fibroblast or amniotic fluid. To our knowledge, patient 1 was the first case diagnosed by using array CGH performed on peripheral lymphocytes in Korea.

A Novel 1.13 Mb Interstitial Duplication at 19q13.32 Causing Developmental Delay and Microcephaly in a Pediatric Patient: the First Asian Case Report

Only 6 patients with partial trisomy of the long arm of chromosome 19 (19q), caused by direct interstitial duplications, have been reported until today. Herein, we report a pediatric patient with a novel 1.13 Mb direct interstitial duplication within 19q13.32, which is the smallest fragment affected so far. A five-year old Korean boy of healthy parents presented with microcephaly, growth retardation, developmental delay, and craniofacial dysmorphism. Even though G-banded chromosome analysis at resolution of 550-band revealed normal karyotype, duplication of 1.13 Mb fragment within 19q13.32 was detected by array comparative genomic hybridization. Comparing with previously reported patients with pure duplication involving 19q as a sole chromosomal abnormality, our case showed the smallest duplication segment with relatively mild degree of clinical features. Our present case might serve as the landmark case among patients with 19q duplication for genotype-phenotype correlation study and further identification of critical region for 19q duplication abnormalities.

Microarray-based comparative genomic hybridization analysis in neonates with congenital anomalies: detection of chromosomal imbalances / Hibridização genômica comparativa baseada em microarranjos em neonatos com anomalias congênitas: detecção de desequilíbrios cromossômicos

OBJECTIVE: To identify chromosomal imbalances by whole-genome microarray-based comparative genomic hybridization (array-CGH) in DNA samples of neonates with congenital anomalies of unknown cause from a birth defects monitoring program at a public maternity hospital. METHODS: A blind genomic analysis was performed retrospectively in 35 stored DNA samples of neonates born between July of 2011 and December of 2012. All potential DNA copy number variations detected (CNVs) were matched with those reported in public genomic databases, and their clinical significance was evaluated. RESULTS: Out of a total of 35 samples tested, 13 genomic imbalances were detected in 12/35 cases (34.3%). In 4/35 cases (11.4%), chromosomal imbalances could be defined as pathogenic; in 5/35 (14.3%) cases, DNA CNVs of uncertain clinical significance were identified; and in 4/35 cases (11.4%), normal variants were detected. Among the four cases with results considered causally related to the clinical findings, two of the four (50%) showed causative alterations already associated with well-defined microdeletion syndromes. In two of the four samples (50%), the chromosomal imbalances found, although predicted as pathogenic, had not been previously associated with recognized clinical entities. CONCLUSIONS: Array-CGH analysis allowed for a higher rate of detection of chromosomal anomalies, and this determination is especially valuable in neonates with congenital anomalies of unknown etiology, or in cases in which karyotype results cannot be obtained. Moreover, although the interpretation of the results must be refined, this method is a robust and precise tool that can be used in the first-line investigation of congenital anomalies, and should be considered for prospective/retrospective analyses of DNA samples by birth defect monitoring programs. .

OBJETIVO: Identificar desequilíbrios cromossômicos por meio da hibridização genômica comparativa baseada em microarranjos (CGH-array) em amostras de DNA de neonatos com anomalias congênitas de causa desconhecida de um programa de monitoramento de defeitos congênitos em uma maternidade pública. MÉTODOS: Uma análise genômica cega foi realizada retrospectivamente em 35 amostras armazenadas de DNA de neonatos nascidos entre julho de 2011 e dezembro de 2012. Todas as possíveis variações no número de cópias (CNVs) de DNA foram comparadas com as relatadas em bases de dados genômicos públicas, e sua relevância clínica foi avaliada. RESULTADOS: De um total de 35 amostras testadas, foram detectados 13 desequilíbrios genômicos em 12/35 casos (34,3%). Em 4/35 casos (11,4%), os desequilíbrios cromossômicos poderiam ser definidos como patogênicos; em 5/35 (14,3%) deles foram identificadas CNVs de DNA de relevância clínica incerta; e, em 4/35 (11,4%), foram detectadas variações normais. Dentre os quatro casos com resultados considerados relacionados causalmente aos achados clínicos, 2/4 (50%) apresentaram alterações causais já relacionadas a síndromes de microdeleção bem definidas. Em 2/4 amostras (50%), os desequilíbrios cromossômicos encontrados, embora preditivos como patogênicos, não estavam relacionados anteriormente a entidades clínicas reconhecidas. CONCLUSÕES: A análise de CGH-array permitiu maior taxa de detecção de anomalias cromossômicas, e essa determinação é valiosa principalmente em neonatos com anomalias congênitas de etiologia desconhecida ou em casos em que os resultados do cariótipo não podem ser obtidos. Além disso, embora a interpretação dos resultados deva ser refinada, esse método é uma ferramenta robusta e precisa que pode ser usada na investigação de primeira linha de anomalias congênitas e deve ser considerada em análises futuras/retrospectivas de amostras de DNA por programas de monitoramento de defeitos congênitos. .

Molecular cytogenetic evaluation of chromosomal microdeletions: the experience of a public hospital in Southern Brazil

Introduction: During the past few decades, the number of diseases identified to be caused by chromosomal microdeletions has increased quickly, bringing a new and crucial role for cytogenetics on the diagnosis of these conditions. The purpose of this study was to identify and characterize chromosomal microdeletions associated with malformation syndromes and intellectual disability. Methods: We retrospectively evaluated a consecutive series of samples from a cohort of 598 subjects with clinical symptoms of a microdeletion syndrome, including the deletion of chromosomes 4p16.3, 5p15.2, 5q35, 7q11.23, 8q24.12, 15q11.2, 16p13.3, 17p13.3, 17p11.2,2, and 22q11.2, as investigated by fluorescence in situ hybridization (FISH). Array-based comparative genomic hybridization (array-CGH) was performed on 25 samples with microdeletions. Results: A total of 598 samples were evaluated from patients whose clinical phenotypes were most indicative of 22q11.2 deletion syndrome (29.10%), Prader-Willi syndrome (23.41%), Angelman syndrome (16.89%), and Williams-Beuren syndrome (14.72%). In 142 of the samples (23.75%), a chromosomal imbalance associated with phenotypic abnormalities was found. The deletion of 7q11.23 was the most frequent (8.03%), followed by del22q11.2 (5.68%) and del15q11.2 (5%). Conclusion: Our study reinforces the idea that the effort to improve the capacity to perform molecular cytogenetic investigations associated with a qualified clinical evaluation is crucial for the detection and precise characterization of submicroscopic chromosome deletions, bringing benefits to patients, relatives, and genetic counselors. It also contributes to the continuing education of cytogeneticists and to the knowledge of chromosomal rearrangements associated with genomic disorders.

A de novo Microdeletion of ANKRD11 Gene in a Korean Patient with KBG Syndrome

KBG syndrome is a very rare genetic disorder characterized by macrodontia of upper central incisors, global developmental delay, distinctive craniofacial features, short stature, and skeletal anomalies. Ankyrin repeat domain 11 gene (ANKRD11) has recently been identified as a causal factor of this syndrome. We describe a 6-yr-old Korean boy with features of KBG syndrome. The patient had a short stature, macrodontia, dysmorphic facial features, speech and motor delay with intellectual disability, and partial seizures as indicated by the electroencephalogram, but he was neither autistic nor had autism spectrum disorders. Using high-resolution oligonucleotide array comparative genomic hybridization, we identified a heterozygous 240-kb deletion at 16q24.3 corresponding to ANKRD11. This patient provided additional evidence on the influence of ANKRD11 in KBG syndrome and suggested that deletion limited to ANKRD11 is unlikely to cause autism.

Ribosomal protein mutations in Korean patients with Diamond-Blackfan anemia

Diamond-Blackfan anemia (DBA) is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, associated physical malformations and a predisposition to cancer. DBA has been associated with mutations and deletions in the large and small ribosomal protein genes, and genetic aberrations have been detected in approximately50-60% of patients. In this study, nine Korean DBA patients were screened for mutations in eight known DBA genes (RPS19, RPS24, RPS17, RPS10, RPS26, RPL35A, RPL5 and RPL11) using the direct sequencing method. Mutations in RPS19, RPS26 and RPS17 were detected in four, two and one patient, respectively. Among the mutations detected in RPS19, two mutations were novel (c.26T>A, c.357-2A>G). For the mutation-negative cases, array-CGH analysis was performed to identify copy-number variations, and no deletions involving the known DBA gene regions were identified. The relative mRNA expression of RPS19 estimated using real-time quantitative PCR analysis revealed two- to fourfold reductions in RPS19 mRNA expression in three patients with RPS19 mutations, and p53 protein expression analysis by immunohistochemistry showed variable but significant nuclear staining in the DBA patients. In conclusion, heterozygous mutations in the known DBA genes RPS19, RPS26 and RPS17 were detected in seven out of nine Korean DBA patients. Among these patients, RPS19 was the most frequently mutated gene. In addition, decreased RPS19 mRNA expression and p53 overexpression were observed in the Korean DBA patients, which supports the hypothesis that haploinsufficiency and p53 hyperactivation represent a central pathway underlying the pathogenesis of DBA.

Clinical features and aCGH analysis of one child with Phelan-McDermid syndrome / 临床儿科杂志

Objective To analyze the clinical features and results of array-comparative genomic hybridization (array CGH, aCGH) in a Chinese girl with Phelan-McDermid syndrome. Methods The clinical symptoms of a child with Phelan-Mc-Dermid syndrome were retrospectively analyzed. Routine G-banding was performed to analyze the karyotype, and the aCGH was used to analyze subchromosomal abnormalities. Results The routine karyotype analysis showed a normal female karyotype without abnomalities in chromosome number and structure. aCGH analysis finely mapped the deletion of Chr22q13.2-qter. Phel-an-McDermid syndrome was diagnosed for this case. Conclusions Phelan-McDermid syndrome can be diagnosed by the typi-cal and detailed clinical features in combination with the laboratory examinations of subchromosomal abnormalities. aCGH is one of the most valuable methods to analyze subchromosomal abnormalities and to diagnose Phelan-McDermid syndrome.

Genome-Wide Analysis of DNA Copy Number Changes in Liver Steatosis.

Aims: Liver steatosis is the most common benign form of non-alcoholic fatty liver disease. It might be a risk factor for hepatocellular carcinoma, either (i) by causing fibrosis, which highly predisposes to hepatoma, or (ii) by being an early precursor of carcinoma, although it is usually considered not to be pre-neoplastic. We investigated the genomic profile of liver samples from patients with fatty liver disease. Study Design & Methodology: Copy number variation was investigated by array-CGH, using the Human Genome 244K catalogue array (Agilent Technologies), and changes validated by quantitative polymerase chain reaction analysis. Results: The analysis of liver biopsies from 17 patients, 10 of whom had histological diagnosis of non-alcoholic fatty liver disease, showed differences in the type of variants in patients with steatosis compared to those without steatosis at several chromosome bands, including 3q29, 6p2, 11q11 and 22q11. Conclusion: The genomic copy number changes we have demonstrated suggest that genomic structural variations may be associated with the pathogenesis or the evolution of steatosis.

De la observación microscópica de los cromosomas en el cariotipo a los array-CGH en el diagnóstico prenatal / From microscopic chromosome observation in karyotyping to array-CGH in prenatal diagnosis

Introducción: el cariotipo ha sido la prueba de oro para el análisis cromosómico en el diagnóstico prenatal en los últimos cuarenta años; sin embargo, a partir del 2011 se publican múltiples artículos y los primeros meta-análisis que muestran posibles ventajas de los array-CGH (del inglés array-comparative genomic hibridization) sobre el cariotipo en el diagnóstico prenatal. Objetivo: hacer una reflexión acerca del uso de array-CGH en el diagnóstico prenatal y mostrar algunas de las potenciales ventajas y desventajas de esta prueba molecular con relación al cariotipo, así como su aplicación por obstetras, perinatólogos y especialistas en medicina materno-fetal. Conclusión: los a-CGH son una nueva alternativa en el análisis cromosómico en el diagnóstico prenatal en fetos con anomalías anatómicas; pueden usarse en todos los casos en que se justifique una intervención invasiva en el diagnóstico prenatal de alteraciones cromosómicas, y es probable que los array-CGH reemplacen al cariotipo en el diagnóstico prenatal en esta década.

Introduction: Karyotyping has been the gold standard for chromosomal analysis in prenatal diagnosis over the past 40 years. However, many articles and the first meta-analysis on the potential advantages of array-CGH (array comparative genomic hybridization) compared to karyotyping in prenatal diagnosis began to appear in 2011. Objective: The objective of this article is to examine the use of array-CGH in prenatal diagnosis, and to show certain potential advantages and disadvantages of this molecular test over karyotyping, as well as its application by obstetricians, perinatologists and specialists in maternal-fetal medicine. Conclusion: Array-CGH is a new option for chromosomal analysis in prenatal diagnosis of fetuses with anatomical abnormalities; it maybe used in all instances where an invasive intervention is warranted in the prenatal diagnosis of chromosomal abnormalities, and it may eventually replace karyotyping in prenatal diagnosis before this decade is out.

Low-frequency Mosaicism of Trisomy 14, Missed by Array CGH

Mosaic trisomy 14 syndrome is a well-known but unusual chromosomal abnormality with a distinct and recognizable phenotype. Array comparative genomic hybridization (CGH) analysis has recently become a widely used method for detecting DNA copy number changes, in place of traditional karyotype analysis. However, the array CGH shows a limitation for detecting the low-level mosaicism. Here, we report the detailed clinical and cytogenetic findings of patient with low-frequency mosaic trisomy 14, initially considered normal based on usual cut-off levels of array CGH, but confirmed by G-banding karyotyping. Our patient had global developmental delay, short stature, congenital heart disease, craniofacial dysmorphic features, and dark skin patches over her whole body. Estimated mosaicism proportion was 23.3% by G-banding karyotyping and 18.0% by array CGH.

Array-Based Comparative Genomic Hybridization in 190 Korean Patients with Developmental Delay and/or Intellectual Disability: A Single Tertiary Care University Center Study

PURPOSE: This study analyzed and evaluated the demographic, clinical, and cytogenetic data [G-banded karyotyping and array-based comparative genomic hybridization (array CGH)] of patients with unexplained developmental delay or intellectual disability at a single Korean institution. MATERIALS AND METHODS: We collected clinical and cytogenetic data based on retrospective charts at Ajou University Medical Center, Suwon, Korea from April 2008 to March 2012. RESULTS: A total of 190 patients were identified. Mean age was 5.1+/-1.87 years. Array CGH yielded abnormal results in 26 of 190 patients (13.7%). Copy number losses were about two-fold more frequent than gains. A total of 61.5% of all patients had copy number losses. The most common deletion disorders included 22q11.2 deletion syndrome, 15q11.2q12 deletion and 18q deletion syndrome. Copy number gains were identified in 34.6% of patients, and common diseases among these included Potocki-Lupski syndrome, 15q11-13 duplication syndrome and duplication 22q. Abnormal karyotype with normal array CGH results was exhibited in 2.6% of patients; theses included balanced translocation (n=2), inversion (n=2) and low-level mosaicism (n=1). Facial abnormalities (p<0.001) and failure to thrive were (p<0.001) also more frequent in the group of patients with abnormal CGH findings. CONCLUSION: Array CGH is a useful diagnostic tool in clinical settings in patients with developmental delay or intellectual disability combined with facial abnormalities or failure to thrive.

Prenatal Diagnosis of der(X)t(X;Y)(p22.31;q11.22) in a Male Fetus by Using Array Comparative Genomic Hybridization

Xp/Yq translocations are rare chromosomal rearrangements, and the phe-notype of male carriers varies according to the segment of the Xp region that is deleted. In this case report, we describe a der(X)t(X;Y)(p22.31;q11.22) translocation, detected by conventional cytogenetic analysis, in a male fetus at a gestational age of 16 weeks. Chromosomal analysis of parental blood confirmed that this chromosomal aberration had been maternally inherited. Array comparative genomic hybridization (CGH) analysis of fetal blood further indicated a nullisomy of Xp22.31-pter and a breakpoint between the STS and KAL1 genes. The STS, NLGN4, ARSE, CSF2RA, and SHOX genes are present in the region that was deleted, and are known to be related to conditions such as X-linked ichthyosis, chondrodysplasia punctata, mental retardation, and facial dysmorphism in humans. Prenatal ultrasonographic findings and autopsy results were consistent with Xp22.31-pter deletion phenotypes. Genetic counseling was provided for the mother. The observations from this case study indicate that advanced molecular techniques can provide a more precise prenatal diagnosis of chromosomal anomalies than conventional cytogenetics can.

Diagnóstico citogenético de pacientes com retardo mental idiopático / Cytogenetic diagnosis of patients with idiopathic mental retardation

O retardo mental é uma condição presente em 2 por cento a 3 por cento da população e mais da metade dos casos ainda são considerados idiopáticos. Sua etiologia é heterogênea e as anomalias cromossômicas têm importante contribuição. A aplicação de técnicas de citogenética clássica e de citogenética molecular tem permitido o diagnóstico preciso em muitos casos, proporcionando melhor acompanhamento clínico e aconselhamento genético. Este trabalho tem como objetivo informar sobre os principais exames atualmente disponíveis para a investigação de rearranjos cromossômicos em pacientes com retardo mental idiopático, incluindo cariótipo com bandeamento G, hibridação in situ fluorescente (FISH), cariotipagem espectral (SKY), amplificação de múltiplas sondas dependente de ligação (MLPA) e hibridação genômica comparativa em array (array-CGH).

Mental retardation is a condition that affects 2 percent-3 percent of the population and more than half of the cases are still deemed idiopathic. Its etiology is heterogeneous and chromosome abnormalities play a significant role. The application of classical cytogenetic and molecular cytogenetic techniques has enabled accurate diagnosis in several cases, which allows better clinical monitoring and genetic counseling. This paper aims at informing about the major tests currently available to investigate chromosome abnormalities in patients with idiopathic mental retardation, including GTG-banded karyotyping, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), multiplex ligation-dependent probe amplification (MLPA) and array-comparative genomic hybridization (array-CGH).

A Case of Near-triploidy in Myelodysplastic Syndrome with del(5q) Combined with del(1p) and del(13q)

Numerical and structural chromosomal abnormalities are common in hematological malignancies. Near-triploidy (58-80 chromosomes) is a numerical abnormality observed in 3% of adult cases of acute lymphoblastic leukemia. Near-triploidy is rare in myeloid lineage hematologic malignancies and compared to near-triploidy in lymphoid malignancies, near-triploidy in myeloid malignancies is associated with poor outcomes. Few studies on near-triploidy in myelodysplastic syndrome (MDS) have been reported, and the clinicopathologic significance of this condition is still unclear. Here, we report a novel case of MDS with near-triploidy and multiple structural chromosomal abnormalities: del(5q) combined with del(1p) and del(13q). These abnormalities were detected by cytogenetic analysis with array comparative genomic hybridization (CGH). Our results suggest that array CGH can be a useful tool for detecting chromosomal abnormalities in patients with MDS.

Reciprocal Deletion and Duplication of 17p11.2-11.2: Korean Patients with Smith-Magenis Syndrome and Potocki-Lupski Syndrome

Deletion and duplication of the -3.7-Mb region in 17p11.2 result in two reciprocal syndrome, Smith-Magenis syndrome and Potocki-Lupski syndrome. Smith-Magenis syndrome is a well-known developmental disorder. Potocki-Lupski syndrome has recently been recognized as a microduplication syndrome that is a reciprocal disease of Smith-Magenis syndrome. In this paper, we report on the clinical and cytogenetic features of two Korean patients with Smith-Magenis syndrome and Potocki-Lupski syndrome. Patient 1 (Smith-Magenis syndrome) was a 2.9-yr-old boy who showed mild dysmorphic features, aggressive behavioral problems, and developmental delay. Patient 2 (Potocki-Lupski syndrome), a 17-yr-old boy, had only intellectual disabilities and language developmental delay. We used array comparative genomic hybridization (array CGH) and found a 2.6 Mb-sized deletion and a reciprocal 2.1 Mb-sized duplication involving the 17p11.2. These regions overlapped in a 2.1 Mb size containing 11 common genes, including RAI1 and SREBF.

Chromosome genetic changes in hepatocellular carcinoma with double exposure to hepatitis B virus/aflatoxin B1 : A preliminary study from Guangxi / 中华肝胆外科杂志

ObjectiveTo study the chromosome genetic changes in hepatocellular carcinoma (HCC) with double exposure to hepatitis B virus/aflatoxin B1 (HBV/AFB1) in Guangxi.Method Differences in genomic alterations in 32 patients with HCC were analyzed using comparative genomic hybridization(CGH).Results(1) The majority of chromosome copy number in the 32 HCC samples had varying degrees of change.The amplification of chromosome regions were 1q,7q,8q,with the high frequency regions being 1q,8q.The deletion of chromosome regions were 1p,4q,8p,9p,13q,14q,16p,16q,17p,18q,19p,Y,with the high frequency regions being 1p,4q,8p,16q,17p,19p;(2) There were also some high copy number amplification or deletion of small regions,such as 2p25.1-p25.2,3q22.3-q23,7p14.1-p14.3,and 9p13.2-9p21; (3) Hierarchical clustering analysis showed that the rate of deletion of chromosome 13q decreased progressively in the following 4 groups:-HBsAg(+)/AFB1 (+),HBsAg(+)/AFB1 (-),HBsAg( - )/AFB1 ( + ),and HBsAg( - )/AFB1 (-) (x2=6.452,P＜0.05).4p was found mainly to be amplified in the HBsAg(+)/AFB1(-)group,but it was mainly deleted in the HBsAg(-)/AFB1(+),and HBsAg( - )/AFB1(-) groups.19q was found mainly to be amplified in the HBsAg(+)/AFB1(+) group,but it was mainly deleted in the HBsAg(-)/AFB1(+),and HBsAg(-)/AFB1(-) groups.ConclusionThe chromosome genetic changes of HCC in Guangxi showed multiplicity.The deletion of chromosome 19p,2p25.1-25.2,3q22.3-q23,7p14.1-p14.3 and amplification of chromosome 9p13.2-9p21 are probably unique genetic characteristics of HCC in this region.The combined effects of Hepatitis B virus and aflatoxin B1 may contribute to deletion of chromosome 13q of HCC in Guangxi.

Molecular Cytogenetic Characterization of Supernumerary Marker Chromosomes by Chromosomal Microarray

PURPOSE: Supernumerary marker chromosome (SMC) could be associated with various phenotypic abnormalities based on the chromosomal origin of SMCs. The present study aimed to determine the genomic contents of SMCs using chromosomal microarray and to analyze molecular cytogenetic characterizations and clinical phenotypes in patients with SMCs. MATERIALS AND METHODS: Among patients with SMCs detected in routine chromosomal analysis, SMCs originating from chromosome 15 were excluded from the present study. CGH-based oligonucleotide chromosomal microarray was performed in 4 patients. RESULTS: The chromosomal origins of SMCs were identified in 3 patients. Case 1 had a SMC of 16.1 Mb in 1q21.1-q23.3. Case 2 showed 21 Mb gain in 19p13.11-q13.12. Case 3 had a 4.5 Mb-sized SMC rearranged from 2 regions of 2.5 Mb in 22q11.1-q11.21 and 2.0 Mb in 22q11.22-q11.23. CONCLUSION: Case 1 presented a wide range of phenotypic abnormalities including the phenotype of 1q21.1 duplication syndrome. In case 2, Asperger-like symptoms are apparently related to 19p12-q13.11, hearing problems and strabismus to 19p13.11 and other features to 19q13.12. Compared with cat-eye syndrome type I and 22q11.2 microduplication syndrome, anal atresia in case 3 is likely related to 22q11.1-q11.21 while other features are related to 22q11.22-q11.23. Analyzing SMCs using high-resolution chromosomal microarray can help identify specific gene contents and to offer proper genetic counseling by determining genotype-phenotype correlations.

Supernumerary Marker Chromosome in a Child with Microcephaly and Mental Retardation.

A de novo supernumerary marker chromosome (SMC) was identified in a 13- month-old girl who presented with microcephaly and mild mental retardation. On further characterization by oligo-nucleotide array-comparative genomic hybridization [array-CGH], the SMC was confirmed to be 18p.

Replication of the Association between Copy Number Variation on 8p23.1 and Autism by Using ASD-specific BAC Array

To discover genetic markers for autism spectrum disorder (ASD), we previously applied genome-wide BAC array comparative genomic hybridization (array-CGH) to 28 autistic patients and 62 normal controls in Korean population, and identified that chromosomal losses on 8p23.1 and on 17p11.2 are significantly associated with autism. In this study, we developed an 8.5K ASD-specific BAC array covering 27 previously reported ASD-associated CNV loci including ours and examined whether the associations would be replicated in 8 ASD patient cell lines of four different ethnic groups and 10 Korean normal controls. As a result, a CNV-loss on 8p23.1 was found to be significantly more frequent in patients regardless of ethnicity (p<0.0001). This CNV region contains two coding genes, DEFA1 and DEFA3, which are members of DEFENSIN gene family. Two other CNVs on 17p11.2 and Xp22.31 were also distributed differently between ASDs and controls, but not significant (p=0.069 and 0.092, respectively). All the other loci did not show significant association. When these evidences are considered, the association between ASD and CNV of DEFENSIN gene seems worthy of further exploration to elucidate the pathogenesis of ASD. Validation studies with a larger sample size will be required to verify its biological implication.