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Copy number variants prioritization after array-CGH analysis - a cohort of 1000 patients.

Carreira IM, Ferreira SI, Matoso E, Pires LM, Ferrão J, Jardim A, Mascarenhas A, Pinto M, Lavoura N, Pais C, Paiva P, Simões L, Caramelo F, Ramos L, Venâncio M, Ramos F, Beleza A, Sá J, Saraiva J, de Melo JB - Mol Cytogenet (2015)

Bottom Line: All the analyzed 1000 patients had at least one CNV independently of its clinical significance.Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B).As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal.

ABSTRACT

Background: Array-based comparative genomic hybridization has been assumed to be the first genetic test offered to detect genomic imbalances in patients with unexplained intellectual disability with or without dysmorphisms, multiple congenital anomalies, learning difficulties and autism spectrum disorders. Our study contributes to the genotype/phenotype correlation with the delineation of laboratory criteria which help to classify the different copy number variants (CNVs) detected. We clustered our findings into five classes ranging from an imbalance detected in a microdeletion/duplication syndrome region (class I) to imbalances that had previously been reported in normal subjects in the Database of Genomic Variants (DGV) and thus considered common variants (class IV).

Results: All the analyzed 1000 patients had at least one CNV independently of its clinical significance. Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B). In approximately 14 % of the patients an imbalance involving known coding genes, but with partially overlapping or low frequency of CNVs described in the DGV was identified (class IIIA). In 10.4 % of the patients a pathogenic CNV that explained the phenotype was identified consisting of: 40 class I imbalances, 44 class II de novo imbalances and 21 class II X-chromosome imbalances in male patients. In 20 % of the patients a familial pathogenic or potentially pathogenic CNV, consisting of inherited class II imbalances, was identified that implied a family evaluation by the clinical geneticists.

Conclusions: As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.

No MeSH data available.


Related in: MedlinePlus

Distribution of all the imbalances according to the genomic size. As the genomic size of the imbalance increases, the number of imbalances from the four classes reduces. Above 3 Mb in size only imbalances belonging to classes I and II are observed. Class IV imbalances are not represented as they are considered benign copy number variations. There is an association with statistical significance (χ2(1) = 40.591; p < 0.001) between classes I and II and sizes above 3 Mb and between classes IIIA and IIIB and sizes below 3 Mb – dashed line
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Fig2: Distribution of all the imbalances according to the genomic size. As the genomic size of the imbalance increases, the number of imbalances from the four classes reduces. Above 3 Mb in size only imbalances belonging to classes I and II are observed. Class IV imbalances are not represented as they are considered benign copy number variations. There is an association with statistical significance (χ2(1) = 40.591; p < 0.001) between classes I and II and sizes above 3 Mb and between classes IIIA and IIIB and sizes below 3 Mb – dashed line

Mentions: The distribution of all the imbalances from the different classes according to genomic size was evaluated (Fig. 2). From the figure analysis we can observe that as the genomic size of the imbalance increases, the probability to find imbalances from the four classes reduces. Above 3 Mb in size we only found imbalances belonging to class I and II. There is an association with statistical significance (χ2(1) = 40.591; p < 0.001) between class I and II and sizes above 3 Mb, and between class IIIA and IIIB and sizes below 3 Mb.Fig. 2


Copy number variants prioritization after array-CGH analysis - a cohort of 1000 patients.

Carreira IM, Ferreira SI, Matoso E, Pires LM, Ferrão J, Jardim A, Mascarenhas A, Pinto M, Lavoura N, Pais C, Paiva P, Simões L, Caramelo F, Ramos L, Venâncio M, Ramos F, Beleza A, Sá J, Saraiva J, de Melo JB - Mol Cytogenet (2015)

Distribution of all the imbalances according to the genomic size. As the genomic size of the imbalance increases, the number of imbalances from the four classes reduces. Above 3 Mb in size only imbalances belonging to classes I and II are observed. Class IV imbalances are not represented as they are considered benign copy number variations. There is an association with statistical significance (χ2(1) = 40.591; p < 0.001) between classes I and II and sizes above 3 Mb and between classes IIIA and IIIB and sizes below 3 Mb – dashed line
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696247&req=5

Fig2: Distribution of all the imbalances according to the genomic size. As the genomic size of the imbalance increases, the number of imbalances from the four classes reduces. Above 3 Mb in size only imbalances belonging to classes I and II are observed. Class IV imbalances are not represented as they are considered benign copy number variations. There is an association with statistical significance (χ2(1) = 40.591; p < 0.001) between classes I and II and sizes above 3 Mb and between classes IIIA and IIIB and sizes below 3 Mb – dashed line
Mentions: The distribution of all the imbalances from the different classes according to genomic size was evaluated (Fig. 2). From the figure analysis we can observe that as the genomic size of the imbalance increases, the probability to find imbalances from the four classes reduces. Above 3 Mb in size we only found imbalances belonging to class I and II. There is an association with statistical significance (χ2(1) = 40.591; p < 0.001) between class I and II and sizes above 3 Mb, and between class IIIA and IIIB and sizes below 3 Mb.Fig. 2

Bottom Line: All the analyzed 1000 patients had at least one CNV independently of its clinical significance.Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B).As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.

View Article: PubMed Central - PubMed

Affiliation: Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal.

ABSTRACT

Background: Array-based comparative genomic hybridization has been assumed to be the first genetic test offered to detect genomic imbalances in patients with unexplained intellectual disability with or without dysmorphisms, multiple congenital anomalies, learning difficulties and autism spectrum disorders. Our study contributes to the genotype/phenotype correlation with the delineation of laboratory criteria which help to classify the different copy number variants (CNVs) detected. We clustered our findings into five classes ranging from an imbalance detected in a microdeletion/duplication syndrome region (class I) to imbalances that had previously been reported in normal subjects in the Database of Genomic Variants (DGV) and thus considered common variants (class IV).

Results: All the analyzed 1000 patients had at least one CNV independently of its clinical significance. Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B). In approximately 14 % of the patients an imbalance involving known coding genes, but with partially overlapping or low frequency of CNVs described in the DGV was identified (class IIIA). In 10.4 % of the patients a pathogenic CNV that explained the phenotype was identified consisting of: 40 class I imbalances, 44 class II de novo imbalances and 21 class II X-chromosome imbalances in male patients. In 20 % of the patients a familial pathogenic or potentially pathogenic CNV, consisting of inherited class II imbalances, was identified that implied a family evaluation by the clinical geneticists.

Conclusions: As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.

No MeSH data available.


Related in: MedlinePlus