Array testing reveals different types of clinically relevant results. A CNV (copy number variant) classification is already proposed and published by several authors.1, 2, 3 However, none of these proposals defined any subcategories of clinically significant findings. We think that defining subcategories is a crucial basis for developing generic consent, if the patients may choose the kind of information they wish to be informed about. Moreover, there is no consensus concerning the name of the category of disease-causing array findings. Some authors call these CNVs ‘clinically relevant’,4 ‘clinically significant’,5 while others speak of ‘pathological findings’6, 7 or ‘pathogenic CNVs’.8 Most authors do not subcategorize the clinically relevant CNVs,9, 10 while others distinguish subtypes of pathogenic CNVs and for instance report microdeletion and microduplication syndromes with reduced penetrance separately.11, 12 Finally, some classify CNVs with reduced penetrance (susceptibility loci) as variants of unknown clinical significance (VOUS).8 CNVs classified as ‘incidental findings’ are also reported in the literature;13 however, many authors do not describe the definition of the term used14, 15 and others simply include such findings in one group of clinically significant array findings.10 A recent review on incidental findings in genetic testing also underlines the problem of unclear definitions and the problematic terminology for this type of results.16
We suggest using a uniform name for disease-causing array findings, namely, pathogenic, which means that ‘the CNV is documented as clinically significant in multiple peer-reviewed publications, even if penetrance and expressivity of the CNV are known to be variable’.1
Based on our experience we recommend using three subcategories of pathogenic array findings: causative array findings, unexpected diagnoses and susceptibility loci for neurodevelopmental disorders (Table 1).
We introduce the term ‘unexpected diagnoses’ for findings that are often classified by others as ‘incidental findings’,13 because they do not fit the phenotype or the indication for testing. The reason for this is that ‘an incidental finding’ means ‘a diagnosis found unintentionally’. In case an affected proband is tested with a whole-genome array technique to detect CNVs, one can hardly describe a pathogenic CNV as unintentional; indeed the aim of array testing is finding CNVs! However, it may represent a pathogenic CNV that does not match the indication or phenotype.
We propose to include susceptibility loci for neurodevelopmental phenotypes in a separate subcategory of pathogenic array findings. It is well established that the incidence of such CNVs among affected individuals is increased in comparison with the general population. Therefore, they may be classified as pathogenic2, 17 in spite of their variable phenotypes and inheritance from normal parents. A susceptibility locus should represent a separate subcategory, as the disorders of extreme phenotypic heterogeneity or variable expressivity probably partly depend on the presence of a second-site variant.18, 19, 20 If a susceptibility locus is found prenatally, the risk for developing the disease is still unquantified and little can be offered in a prenatal setting, as neurodevelopmental phenotypes most often cannot be ascertained by ultrasound examination.
Deletions revealing carrier status for recessive diseases may also be found in array testing and these are a separate category of findings. According to the American College of Medical Genetics1 comprehensive reporting of heterozygous recessive mutations is outside the scope of genomic array testing and, in general, is not recommended. It is also not feasible to check all genes in large deletions. However, there are some situations when reporting such findings is clinically important. We do agree with Kearney et al.1 that carrier status in case of a well-characterized recessive disorder with a reasonably high population frequency and/or with clinical features consistent with the patient’s reason for referral, may be considered for disclosure.21
We recommend using the term incidental findings for a separate category of pathogenic array findings that are found in the parents. Targeted array testing of parental DNA can be performed in both prenatal and postnatal settings to determine inheritance of CNVs found in the proband. If by chance a pathogenic abnormality in the parental array profile is found, such a finding is truly incidental as array diagnosis is not meant to find pathogenic abnormalities in the parents. These incidental findings do not particularly refer to the target regions, which were the indication for testing, but to other findings encountered by chance (Table 1, last row), for example during the quality control of the array profiles.
Finally, as SNP arrays are nowadays more often employed in diagnostic settings, not only CNVs but also abnormal B-allelic frequencies can indicate a pathogenic finding.22 Therefore, we suggest broadening the classification to array findings and not narrowing it to CNVs only. Moreover, the proposed classification is generic and potentially may also be applicable for massive parallel sequencing (MPS) findings.
If the classification is to contribute to generic consent, based on which a patient may choose which information he/she wishes to be informed about, the subcategory of pathogenic unexpected diagnoses should be further divided into subclasses as suggested in Table 1. Otherwise such a heterogeneous subcategory might be misunderstood by patients leading to incorrect choices and frustrations if a certain pathogenic array finding is not reported.
An international classification and terminology for array findings are indispensable in order to avoid miscommunication, to facilitate comparing cohorts studied by different researchers and to optimize pre-test counseling. We hope that our suggestion will contribute to the establishment of a generic array and ultimately also to MPS findings classification.
References
Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST : Working Group of the American College of Medical Genetics Laboratory Quality Assurance C: American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 2011; 13: 680–685.
Kaminsky EB, Kaul V, Paschall J et al: An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genet Med 2011; 13: 777–784.
Riggs ER, Church DM, Hanson K et al: Towards an evidence-based process for the clinical interpretation of copy number variation. Clin Genet 2012; 81: 403–412.
Faas BH, Feenstra I, Eggink AJ et al: Non-targeted whole genome 250K SNP array analysis as replacement for karyotyping in fetuses with structural ultrasound anomalies: evaluation of a one-year experience. Prenat Diagn 2012; 32: 362–370.
Rooryck C, Toutain J, Cailley D et al: Prenatal diagnosis using array-CGH: a French experience. Eur J Med Genet 2013; 56: 341–345.
Lee CN, Lin SY, Lin CH, Shih JC, Lin TH, Su YN : Clinical utility of array comparative genomic hybridisation for prenatal diagnosis: a cohort study of 3171 pregnancies. BJOG 2012; 119: 614–625.
Leung TY, Vogel I, Lau TK et al: Identification of submicroscopic chromosomal aberrations in fetuses with increased nuchal translucency and apparently normal karyotype. Ultrasound Obstet Gynecol 2011; 38: 314–319.
Wapner RJ, Martin CL, Levy B et al: Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012; 367: 2175–2184.
Srebniak MI, Boter M, Oudesluijs GO et al: Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities. Mol Cytogenet 2012; 5: 14.
Fiorentino F, Caiazzo F, Napolitano S et al: Introducing array comparative genomic hybridization into routine prenatal diagnosis practice: a prospective study on over 1000 consecutive clinical cases. Prenat Diagn 2011; 31: 1270–1282.
Scott F, Murphy K, Carey L et al: Prenatal diagnosis using combined quantitative fluorescent polymerase chain reaction and array comparative genomic hybridization analysis as a first-line test: results from over 1000 consecutive cases. Ultrasound Obstet Gynecol 2013; 41: 500–507.
Shaffer LG, Dabell MP, Fisher AJ et al: Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn 2012; 32: 976–985.
Boone PM, Soens ZT, Campbell IM et al: Incidental copy-number variants identified by routine genome testing in a clinical population. Genet Med 2013; 15: 45–54.
Vestergaard EM, Christensen R, Petersen OB, Vogel I : Prenatal diagnosis: array comparative genomic hybridization in fetuses with abnormal sonographic findings. Acta Obstet Gynecol Scand 2013; 92: 762–768.
Hillman SC, McMullan DJ, Hall G et al: Prenatal chromosomal microarray use: a prospective cohort of fetuses and a systematic review and meta-analysis. Ultrasound Obstet Gynecol 2013; 41: 610–620.
Christenhusz GM, Devriendt K, Dierickx K : To tell or not to tell? A systematic review of ethical reflections on incidental findings arising in genetics contexts. Eur J Hum Genet 2013; 21: 248–255.
Cooper GM, Coe BP, Girirajan S et al: A copy number variation morbidity map of developmental delay. Nat Genet 2011; 43: 838–846.
Veltman JA, Brunner HG : Understanding variable expressivity in microdeletion syndromes. Nat Genet 2010; 42: 192–193.
Girirajan S, Rosenfeld JA, Cooper GM et al: A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet 2010; 42: 203–209.
Girirajan S, Rosenfeld JA, Coe BP et al: Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med 2012; 367: 1321–1331.
McDonald-McGinn DM, Fahiminiya S, Revil T et al: Hemizygous mutations in SNAP29 unmask autosomal recessive conditions and contribute to atypical findings in patients with 22q11.2DS. J Med Genet 2013; 50: 80–90.
Bruno DL, White SM, Ganesamoorthy D et al: Pathogenic aberrations revealed exclusively by single nucleotide polymorphism (SNP) genotyping data in 5000 samples tested by molecular karyotyping. J Med Genet 2011; 48: 831–839.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no conflict of interest.
Rights and permissions
About this article
Cite this article
Srebniak, M., Diderich, K., Govaerts, L. et al. Types of array findings detectable in cytogenetic diagnosis: a proposal for a generic classification. Eur J Hum Genet 22, 856–858 (2014). https://doi.org/10.1038/ejhg.2013.254
Published:
Issue Date:
DOI: https://doi.org/10.1038/ejhg.2013.254
This article is cited by
-
Copy number variations in ultrasonically abnormal late pregnancy fetuses with normal karyotypes
Scientific Reports (2020)
-
Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies
Biochemical Genetics (2020)
-
Choosing between Higher and Lower Resolution Microarrays: do Pregnant Women Have Sufficient Knowledge to Make Informed Choices Consistent with their Attitude?
Journal of Genetic Counseling (2018)
-
Chromosomal microarray testing in adults with intellectual disability presenting with comorbid psychiatric disorders
European Journal of Human Genetics (2017)
-
Prenatal SNP array testing in 1000 fetuses with ultrasound anomalies: causative, unexpected and susceptibility CNVs
European Journal of Human Genetics (2016)