Frequent detection of parental consanguinity in children with developmental disorders by a combined CGH and SNP microarray
© Fan et al.; licensee BioMed Central Ltd. 2013
Received: 15 July 2013
Accepted: 28 August 2013
Published: 20 September 2013
Genomic microarrays have been used as the first-tier cytogenetic diagnostic test for patients with developmental delay/intellectual disability, autism spectrum disorders and/or multiple congenital anomalies. The use of SNP arrays has revealed regions of homozygosity in the genome which can lead to identification of uniparental disomy and parental consanguinity in addition to copy number variations. Consanguinity is associated with an increased risk of birth defects and autosomal recessive disorders. However, the frequency of parental consanguinity in children with developmental disabilities is unknown, and consanguineous couples may not be identified during doctor’s visit or genetic counseling without microarray.
We studied 607 proband pediatric patients referred for developmental disorders using a 4 × 180 K array containing both CGH and SNP probes. Using 720, 360, 180, and 90 Mb as the expected sizes of homozygosity for an estimated coefficient of inbreeding (F) 1/4, 1/8, 1/16, 1/32, parental consanguinity was detected in 21cases (3.46%).
Parental consanguinity is not uncommon in children with developmental problems in our study population, and can be identified by use of a combined CGH and SNP chromosome microarray. Identification of parental consanguinity in such cases can be important for further diagnostic testing.
KeywordsChromosome microarray Consanguinity Developmental disabilities
Studies of the human genome using genomic arrays (also called chromosomal microarrays) in the last decade have revolutionized clinical cytogenetics and changed the standard of care in medical genetics [1–4]. The resolution of the studies has evolved from the megabase level of the bacterial artificial chromosome (BAC) arrays during the early 2000s to the kilobase or exon level of the current oligonucleotide arrays. The traditional microarrays were designed for detection of gene copy number variations (CNVs) by comparative genomic hybridization (CGH), and were popularly called CGH arrays. The second type of arrays containing a high density of probes for single nucleotide polymorphisms (SNPs), so called SNP array, reveals both CNVs and homozygosity in the genome. The third type of genomic arrays uses a combination of probes designed to detect CNVs and probes to genotype SNPs. The use of genomic microarrays has significantly improved accuracy and diagnostic yield in comparison with the conventional karyotype. Recently, genomic microarrays have been used as the first-tier cytogenetic diagnostic test for patients with developmental delay/intellectual disability, autism spectrum disorders and/or multiple congenital anomalies [2–4]. Many studies have shown the advantages of genomic arrays in detecting pathogenic CNVs. Our laboratory has performed CGH array studies on about 2500 patients with developmental disorders since 2005, and reported a 14% detection rate for pathogenic CNVs [5, 6].
The use of SNP arrays has revealed regions of homozygosity (ROH) in the genome which can lead to identification of uniparental disomy (UPD) and parental consanguinity in addition to CNVs [7, 8]. It is well known that consanguinity is associated with an increased risk of congenital anomalies and autosomal recessive diseases [9–12]. The recently published Geneva International Consanguinity Workshop report discussed the health impact of consanguinity and highlighted the importance of evidence-based counseling recommendations for consanguineous marriage and for undertaking genomic and social research in defining the various influences and outcomes of consanguinity . However, the frequency of parental consanguinity in children with developmental disabilities is unknown, and consanguineous couples may not be identified during doctor’s visit or genetic counseling without microarray study as our data have shown. Here we report our study results on patients referred for developmental problems using a combined CGH/SNP array with a focus on detection of parental consanguinity.
Summary of array study results
No. of proband patients
No. of cases with pathogenic CNV (%)
No. of cases with UPD (%)
No. of cases with ROH ≥68 Mb (%)
The cases with parental consanguinity
Size of HZ (Mb)
Estimated coefficient of inbreeding (F)
Post-testing information on mating type
DD, DE, DF,RA
DF, CA, RF
DD, DF, FT
From the same small town
ID, GR, SS
In addition to pathogenic CNVs and UPDs, approximately 3.5% of children with intellectual and/or developmental disabilities in our study populations showed greater than 68 Mb of ROH, suggesting presence of parental consanguinity. Post-testing surveys confirmed the 1st cousin relationships for all the cases with an estimated F 1/16 and presence of consanguinity in 4 out of 5 cases with an estimated F1/32 although the information from medical records was incomplete or inconsistent with the suggested mating type. In our practice, we report results suggesting presence of parental consanguinity but not specify the biological relationship of the parents as recommended by the ACMG guidelines , because SNP array analysis is not designed to be a paternity test or to assign a specific relationship between the parents of the proband patient. Also, the observed size of ROH may not precisely predict the true biological relationship due to variables such as recombination during meiosis, multiple loops of consanguinity or multiple generations of breeding within a relatively closed community. For the patients showing an estimated F ¼ or 1/8, we have included the percentage of homozygosity in our clinical report and stated that the result may suggest a first- or second-degree parental relationship or incestuous mating.
Incestuous parental relationships identified by SNP-based microarrays have been reported previously. One was a 3-year-old boy with multiple medical conditions showing 668 Mb of genomic homozygosity which was consistent with the patient being conceived as the product of a mating between first-degree relatives . In a report on a SNP data, ROH of greater than 20% of the genome were identified in two of 5000 samples analyzed in a cytogenetics laboratory in Australia . Our study has shown that a level of ROH greater than 20% correlates with an estimated coefficient of inbreeding F1/4 which is suggestive of a first degree relationship such as parent–child or brother-sister mating, as exemplified in case 001. However, an incestuous relationship, which represents a complicated social and legal issue, may not be readily identified during a doctor’s visit or genetic counseling, as shown in our post-testing survey. Genetic counseling for consanguinity can be complicated particularly when incestuous mating is uncovered by use of microarrays.
The frequency of consanguineous mating may vary significantly in different geographic regions or in different ethnic populations [12, 15–17]. Our study patients were referred from hospitals in South Florida (mainly Miami-Dade and Broward counties) and Brazil. Hispanic or Latino Americans account for 65% of the population in Miami-Dade and 25% of the population in Broward (2010 census data). The Hispanic or Latino Americans in Florida originate mainly from Cuba (32%) and Puerto Rico (28%) and Mexico (9%). It was estimated in 2008 that over one million of Brazilians live in USA and about 300,000 of them live in Florida. First cousin marriage is legal in Florida. The rate of consanguineous marriage in Miami-Dade and Broward counties is unknown but is likely to be higher than the generally estimated average (<1%) in USA. The rate of consanguineous mating in Brazil was estimated as 1.6% with a heterogeneous geographic distribution and half of the consanguineous marriages have a coefficient of inbreeding F 1/16 or higher . There was a consensus that consanguineous marriages are associated with an increased risk of congenital malformations and autosomal recessive disease . The estimated excess risks of morbidity and precocious mortality for the children with F1/4, 1/8, 1/16 and 1/32 are about 40%, 20%, 10%, 5%, respectively [9, 10]. A recent review suggests that the risk for congenital heart disease is increased in consanguineous marriages .
Different from previous clinical studies on the families with a history of consanguineous mating, we detected parental consanguinity in about 3.5% of children referred for developmental problems. Most of these children were referred for congenital anomalies or multiple malformations, developmental delay or intellectual disability, dysmorphic features, failure to thrive/growth retardation or short stature. The finding of parental consanguinity in these cases is highly suggestive of an underlying recessive cause. For example, following the array study, case 012 was diagnosed with Schimke immune-osseous dysplasia, an autosomal-recessive pleiotropic disorder caused by loss of function mutations in SMARCAL1 leading to spondyloepiphyseal dysplasia, renal dysfunction and T-cell immunodeficiency [20, 21]. A diagnosis of autosomal recessive spinal muscular atrophy has been suspected in case 009. In case 001, the 6 year-old girl initially referred for mental problems had a history of proximal renal tubular acidosis (RTA) at 18 months of age, basal ganglia and corneal calcifications secondary to RTA. Further diagnostic work-up has revealed increased excretion of Krebs cycle intermediate and a tentative diagnosis of 2-ketoglutarate dehydrogenase deficiency, a very rare metabolic disorder [22–24]. Involvement of multiple recessive mutant genes or a complex genetic mechanism is possible in some patients, particularly in the children as products of incestuous mating. Consanguinity may not be noted in many cases without microarray studies and identification of the biological relationship of the parents in such cases is clinically important for additional diagnostic testing. Further studies of phenotype and possible correlating metabolic deficiency, as well as sequencing of the ROH regions would determine the genetic mechanisms of the developmental problems in these children.
Patients, all pediatric but one, included in this report were referred for developmental delay or intellectual disability, autism spectrum disorders, and/or congenital anomalies from November 1, 2011 to March 5, 2013. Approximately 80% of the patient samples originated in the Genetics Clinic at the University Miami and other hospitals in south Florida. However, many of the patients were of Latin American or Caribbean descent or referred from Latin American countries. The remaining 20% of patient samples were received from Brazil.
A combined CGH and SNP array, Agilent SurePrint G3 4 × 180 K (Agilent, Santa Clara, USA) has been used in our laboratory as a clinical test for over a year. The array contains 180,000 oligonucleotide probes, including approximately 120,000 CGH probes and 60,000 SNP probes with a resolution of 5 ~ 10 Mb for ROH detection. Array studies were performed using a protocol recommended by Agilent. Briefly, DNA was prepared from a blood sample and purified using the QIAamp DNA Blood Midi Kit (Qiagen) or DNeasy Blood & Tissue Kit (Qiagen) when a sample was less than 0.5 ml. DNA was quantified, digested and then labeled with Cy5 (testing DNA) and Cy3 (reference DNA) and hybridized to the microarray at 65°C for 21 ~ 24 hours. The microarray was washed and analyzed using an Agilent C microarray scanner and CytoGenomics Edition 126.96.36.199 software.
Criteria for reporting
Theoretic size of ROH for coefficient of inbreeding (F) expected from the total 2881 Mb autosomal genome (GRCh37/hg19)
Degree of relationship
Coefficient of inbreeding (F)
Theoretic proportion of identical by decent (%)
Expected ROH size and range (Mb)
720 (540 ~ 1080)
Uncle-niece/aunt-nephew/double half cousins
360 (270 ~ 539)
First cousins/half uncle-niece
180 (135 ~ 269)
Half first cousins/first cousins once removed
90 (68 ~ 134)
Retrospective survey on parental consanguinity
Referring clinicians were contacted to obtain information on the parent’s family relationship of the children for whom laboratory results suggested presence of parental consanguinity. The clinician provided information based on either the notes of clinical geneticists or family history in medical records. In some cases, we obtained information on patient diagnosis after microarray study.
This report is a summary of clinical cases tested in a CLIA certified and Florida State licensed clinical laboratory with patients identification removed. This is not an experimental research using human material and therefore no IRB approval is necessary.
Written informed consent was obtained from the patient’s guardian/parent/next of kin for the publication of this report and any accompanying images.
American college of medical genetics
Bacterial artificial chromosome
Comparative genomic hybridization
Copy number variation
Coefficient of inbreeding
Single nucleotide polymorphisms
Regions of homozygosity
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