American College of Medical Genetics guideline on the cytogenetic evaluation of the individual with developmental delay or mental retardation

The perils of SNP microarray testing: uncovering unexpected consanguinity

BACKGROUND

Although single nucleotide polymorphism chromosomal microarrays identify areas of small genetic deletions or duplications, they can also reveal regions of homozygosity indicative of consanguinity. As more nongeneticists order single nucleotide polymorphism microarrays, they must prepare for the potential ethical, legal, and social issues that result from revelation of unanticipated consanguinity.

PATIENT

We describe an infant with multiple congenital anomalies who underwent single nucleotide polymorphism microarray testing.

RESULTS

The results of the single nucleotide polymorphism microarray revealed several large regions of homozygosity that indicated identity by descent most consistent with a second-degree or third-degree relative mating (e.g., uncle/niece, half-brother/sister, first cousins). The mother was not aware of the test's potential to reveal consanguinity. When informed of the test results, she reluctantly admitted to being raped by her half-brother around the time of conception.

CONCLUSIONS

During the pretesting consent process, providers should inform parents that single nucleotide polymorphism microarray testing could reveal consanguinity. Providers must also understand the psychological implications, as well as the legal and moral obligations, that accompany single nucleotide polymorphism microarray results that indicate consanguinity.

ACMG Standards and Guidelines for fragile X testing: a revision to the disease-specific supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics

Molecular genetic testing of the FMR1 gene is commonly performed in clinical laboratories. Mutations in the FMR1 gene are associated with fragile X syndrome, fragile X tremor ataxia syndrome, and premature ovarian insufficiency. This document provides updated information regarding FMR1 gene mutations, including prevalence, genotype-phenotype correlation, and mutation nomenclature. Methodological considerations are provided for Southern blot analysis and polymerase chain reaction amplification of the FMR1 gene, including triplet repeat-primed and methylation-specific polymerase chain reaction. In addition to report elements, examples of laboratory reports for various genotypes are also included.

Evaluation of the young children with neurodevelopmental disability: a prospective study at hamadan university of medical sciences clinics

OBJECTIVE

Developmental impairment is a common problem in children health that occurs in approximately 5-10% of the childhood population. The aim of this study was to determine the etiologic yield of subspecialists' evaluation of young children with developmental disability.

MATERIALS & METHODS

All children aged between 2 months and 5 years referred over a 15-month period to Hamadan University of Medical Sciences subspecialty services for initial evaluation of a suspected developmental Disability, were enrolled in the present study. Diagnostic yield was determined after the completion of clinical assessments and laboratory tests requested by the evaluating physician.

RESULTS

A total of 198 children (129 boys and 69 girls) were eligible for our study. 108 children had global developmental delay and 90 children had isolated developmental delay. Approximately ¼ of all patients did not have any specific etiology for developmental disability. Cerebral palsy (CP) was the most common clinical syndrome in all patients (41.4%). Hypoxic ischemic encephalopathy (13.8%), brain dysgenesis (13%), genetic disorder (13%), and neurodegenerative diseases (11%) were determined in more than one half of all children with global developmental disability. in our study, "developmental speech delay" was the common cause of isolated speech delay.

CONCLUSION

Determination of an underlying etiology is an essential part of specialty evaluation of young children with developmental disability. The results of this study were similar closely to the results of other studies.

Aetiologic spectrum of mental retardation & developmental delay in India

BACKGROUND & OBJECTIVES

The aetiology of mental retardation is varied and difficult to establish. Reports from India on the spectrum of underlying causative conditions are lacking. This retrospective study was conducted to establish the various aetiologies of mental retardation (MR) and developmental delay (DD) in patients attending a medical genetics centre in north India and to assess the contribution of genetic disorders.

METHODS

This retrospective study was conducted at a tertiary care centre in north India. All patients attending the centre with MR or DD from January 2007 to December 2009 were included. The aetiology of MR/DD was ascertained after clinical assessment and targeted laboratory evaluation. The spectrum of causative conditions and contribution of genetic disorders was established.

RESULTS

A total of 338 patients were included in the study, of whom definite diagnosis was established in 253 (74.8%). The various aetiological categories were: chromosomal disorders in 112 (33.1%), non chromosomal syndromes in 32 (9.5%), neurometabolic disorders in 34 (10.1%), central nervous system structural defects in 25 (7.4%), cerebral palsy in 43 (12.7%) and environmental insults in 7 (2%). Eighty five patients (25.2%) had idiopathic mental retardation. A total of 196 (58%) patients had a genetic disorder as the cause of MR/DD.

INTERPRETATION & CONCLUSIONS

The aetiology of MR/DD is varied and difficult to establish in a significant proportion of patients. Chromosomal and various monogenic disorders contribute to a large number of MR/DD cases and hence a genetic work up is essential for all such patients.

Rapid aneuploidy diagnosis of partial trisomy 7q (7q34→qter) and partial monosomy 10q (10q26.12→qter) by array comparative genomic hybridization using uncultured amniocytes

OBJECTIVE

To present rapid aneuploidy diagnosis (RAD) of partial trisomy 7q (7q34→qter) and partial monosomy 10q (10q26.12→qter) by array comparative genomic hybridization (aCGH) using uncultured amniocytes.

CASE REPORT

A 34-year-old, gravida 2, para 1, woman underwent amniocentesis at 20 weeks of gestation because of a previous mentally retarded child with an unbalanced reciprocal translocation inherited from the carrier father who had a karyotype of 46,XY,t(7;10) (q34;q26.12). Her first child was initially found to have a normal karyotype by routine cytogenetic analysis, but a cryptic chromosomal abnormality was subsequently diagnosed by aCGH. During this pregnancy, RAD by oligonucleotide-based aCGH using uncultured amniocytes revealed a 16.4-Mb duplication of 7q34-q36.3 and a 12.7-Mb deletion of 10q26.12-q26.3. Conventional cytogenetic analysis using cultured amniocytes revealed a karyotype of 46,XX,der(10)t(7;10)(q34;q26.12)pat. The parents elected to terminate the pregnancy. A malformed female fetus was delivered with a high prominent forehead, hypertelorism, epicanthic folds, a broad depressed nasal bridge, a prominent nose with anteverted nostrils, micrognathia, a short neck, large low-set ears, clinodactyly, small big toes, and normal female external genitalia.

CONCLUSION

aCGH is a useful tool for RAD of subtle chromosomal rearrangements in pregnancy, especially under the circumstance of a previous abnormal child with an unbalanced translocation derived from a parental subtle reciprocal translocation.

Clinical utility of array comparative genomic hybridisation for prenatal diagnosis: a cohort study of 3171 pregnancies

OBJECTIVE

To evaluate the clinical value of prenatal array comparative genomic hybridisation (CGH) in screening for submicroscopic genomic imbalances.

DESIGN

Cross-sectional study.

SETTING

Tertiary referral centre.

POPULATION

From June 2008 to February 2011, 3171 fetuses underwent prenatal array CGH testing and karyotyping at the National Taiwan University Hospital. Indications for invasive prenatal diagnosis included abnormal karyotype, abnormal ultrasound, advanced maternal age and parental anxiety.

METHODS

In all, 2497 fetuses were screened with 1-Mb resolution bacterial artificial chromosome array-based CGH, and 674 fetuses with 60-K oligonucleotide array-based CGH. Multiplex ligation-dependent probe amplification, fluorescence in situ hybridization, or 105-K oligonucleotide array CGH provided further confirmation.

MAIN OUTCOME MEASURE

Copy number variations identified by array CGH.

RESULTS

Array CGH detected numerical chromosome anomalies in 37 (1.2%) fetuses, microdeletion/duplication in 34 (1.1%) fetuses, large deletion/duplication in 13 (0.4%) fetuses, benign copy number changes in 13 (0.4%) fetuses and variation of unknown clinical significance in five (0.2%) fetuses. Array CGH was effective in identifying submicroscopic genomic imbalance in fetuses with de novo balance translocations (2/17, 1.8%), supernumerary marker chromosomes (3/6, 50%), and abnormal prenatal ultrasound findings (33/194, 17.0%). Array CGH detected microdeletions/duplications in 12 fetuses with normal karyotype.

CONCLUSION

Prenatal array CGH is effective in screening for submicroscopic genomic imbalance. Array CGH may add 8.2% to the diagnostic field, compared with conventional karyotyping, for fetuses with abnormal ultrasound results, and is particularly useful in fetuses with karyotypic balanced translocation or marker chromosomes. There is a 0.52% baseline risk of submicroscopic genomic imbalance, even in women with an uneventful prenatal examination.

Array comparative genomic hybridization and cytogenetic analysis in pediatric acute leukemias

Most patients with acute lymphocytic leukemia (all) are reported to have acquired chromosomal abnormalities in their leukemic bone marrow cells. Many established chromosome rearrangements have been described, and their associations with specific clinical, biologic, and prognostic features are well defined. However, approximately 30% of pediatric and 50% of adult patients with all do not have cytogenetic abnormalities of clinical significance. Despite significant improvements in outcome for pediatric all, therapy fails in approximately 25% of patients, and these failures often occur unpredictably in patients with a favorable prognosis and "good" cytogenetics at diagnosis.It is well known that karyotype analysis in hematologic malignancies, although genome-wide, is limited because of altered cell kinetics (mitotic rate), a propensity of leukemic blasts to undergo apoptosis in culture, overgrowth by normal cells, and chromosomes of poor quality in the abnormal clone. Array comparative genomic hybridization (acgh-"microarray") has a greatly increased genomic resolution over classical cytogenetics. Cytogenetic microarray, which uses genomic dna, is a powerful tool in the analysis of unbalanced chromosome rearrangements, such as copy number gains and losses, and it is the method of choice when the mitotic index is low and the quality of metaphases is suboptimal. The copy number profile obtained by microarray is often called a "molecular karyotype."In the present study, microarray was applied to 9 retrospective cases of pediatric all either with initial high-risk features or with at least 1 relapse. The conventional karyotype was compared to the "molecular karyotype" to assess abnormalities as interpreted by classical cytogenetics. Not only were previously undetected chromosome losses and gains identified by microarray, but several karyotypes interpreted by classical cytogenetics were shown to be discordant with the microarray results. The complementary use of microarray and conventional cytogenetics would allow for more sensitive, comprehensive, and accurate analysis of the underlying genetic profile, with concomitant improvement in prognosis and treatment, not only for pediatric all, but for neoplastic disorders in general.

Downsizing genomic medicine: approaching the ethical complexity of whole-genome sequencing by starting small

As we look to a time when whole-genome sequencing is integrated into patient care, it is possible to anticipate a number of ethical challenges that will need to be addressed. The most intractable of these concern informed consent and the responsible management of very large amounts of genetic information. Given the range of possible findings, it remains unclear to what extent it will be possible to obtain meaningful patient consent to genomic testing. Equally unclear is how clinicians will disseminate the enormous volume of genetic information produced by whole-genome sequencing. Toward developing practical strategies for managing these ethical challenges, we propose a research agenda that approaches multiplexed forms of clinical genetic testing as natural laboratories in which to develop best practices for managing the ethical complexities of genomic medicine.

Clinical implementation of whole-genome array CGH as a first-tier test in 5080 pre and postnatal cases

Background

Array comparative genomic hybridization (CGH) is currently the most powerful method for detecting chromosomal alterations in pre and postnatal clinical cases. In this study, we developed a BAC based array CGH analysis platform for detecting whole genome DNA copy number changes including specific micro deletion and duplication chromosomal disorders. Additionally, we report our experience with the clinical implementation of our array CGH analysis platform. Array CGH was performed on 5080 pre and postnatal clinical samples from patients referred with a variety of clinical phenotypes.

Results

A total of 4073 prenatal cases (4033 amniotic fluid and 40 chorionic villi specimens) and 1007 postnatal cases (407 peripheral blood and 600 cord blood) were studied with complete concordance between array CGH, karyotype and fluorescence in situ hybridization results. Among 75 positive prenatal cases with DNA copy number variations, 60 had an aneuploidy, seven had a deletion, and eight had a duplication. Among 39 positive postnatal cases samples, five had an aneuploidy, 23 had a deletion, and 11 had a duplication.

Conclusions

This study demonstrates the utility of using our newly developed whole-genome array CGH as first-tier test in 5080 pre and postnatal cases. Array CGH has increased the ability to detect segmental deletion and duplication in patients with variable clinical features and is becoming a more powerful tool in pre and postnatal diagnostics.

Cystic fibrosis carrier screening in obstetric clinical practice: knowledge, practices, and barriers, a decade after publication of screening guidelines

PURPOSE

Cystic fibrosis (CF) carrier screening guidelines have been in place for almost a decade. The purpose of this study was to determine the current awareness by obstetricians of the existence and content of practice guidelines, the variety in practice regarding CF carrier screening, and the level of knowledge regarding CF genetics and screening result interpretation. We also explored potential barriers to offering screening and whether academic affiliation or type of practice influenced outcome.

METHODS

An online survey program was used to deliver a questionnaire to obstetricians throughout the United States. One hundred fifty-six respondents participated, with 143 answering all questions in the survey.

RESULTS

Although most obstetricians are aware of screening guidelines and have accurate knowledge about CF carrier screening, 12.3% were not aware of carrier screening guidelines, 17.7% were unable to interpret basic results, 16.5% experienced barriers to offering screening, and 43% lacked information regarding carrier rates, screening sensitivity, and residual risk.

CONCLUSION

Most obstetricians offer CF carrier screening and will refer to genetic counseling services at times. However, we identified a deficiency of information in a concerning percentage of practitioners. This deficiency could be improved by targeted and readily accessible educational efforts, especially for obstetricians not affiliated with academia.

Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation

BACKGROUND

Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their comparative performance in a clinical context.

METHODS

We studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500 K GeneChip SNP arrays, Agilent Human Genome 244 K oligonucleotide arrays and NimbleGen 385 K Whole-Genome oligonucleotide arrays. We also determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32 K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP arrays.

RESULTS

The Affymetrix 500 K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosomal CNVs in the 30 trios. 147 of these CNVs appeared to be de novo, but only 34 (22%) were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 most likely pathogenic and 2 possibly pathogenic CNVs for MR. All 9 of these putatively pathogenic CNVs were detected by the Affymetrix 500 K, Agilent, NimbleGen and the Illumina arrays, and 5 were found by the SMRT BAC array. Both putatively pathogenic CNVs identified in the 15 trios tested with the Affymetrix 6.0 were identified by this platform.

CONCLUSIONS

Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology.

Microarray analysis in children with developmental disorder or epilepsy

The technique of chromosomal microarray analysis identifies genetic imbalance. Evaluation of its diagnostic role in pediatrics is still underway. We describe our experience with chromosomal microarrays. We retrospectively reviewed the charts of children in the Sections of Neurology and Clinical Genetics at St. Christopher's Hospital for Children who had undergone microarray analysis between 2006 and 2009. Collected data included age, sex, and the presence of mental retardation, developmental delay, autism, learning disability, hypotonia, dysmorphic features, and epilepsy, and the use of microarray technique. Statistical analysis was performed using SPSS. There were 82 children (mean age ± S.D., 5.7 ± 5 years), including 45 (55%) boys and 37 (45%) girls. All patients exhibited a normal karyotype. Microarray analysis produced abnormal results in 20 (23.5%). Deletions comprised 74% of all abnormalities. Patients with ≥ 4 clinical variables demonstrated a 30.5% incidence of abnormal chromosomal microarray findings, compared with 8.7% of patients with ≤ 3 clinical variables (P = 0.039, χ(2) test). Logistic regression indicated that motor impairment (P = 0.039) and presence of epilepsy (P = 0.024) independently contributed to the model. The likelihood of an abnormal microarray result increased with the number of clinical abnormalities. Microarray analysis will likely become the diagnostic genetic test of choice in children with neurodevelopmental disorders or epilepsy.

Submicroscopic subtelomeric aberrations in Chinese patients with unexplained developmental delay/mental retardation

BACKGROUND

Subtelomeric imbalance is widely accepted as related to developmental delay/mental retardation (DD/MR). Fine mapping of aberrations in gene-enriched subtelomeric regions provides essential clues for localizing critical regions, and provides a strategy for identifying new candidate genes. To date, no large-scale study has been conducted on subtelomeric aberrations in DD/MR patients in mainland China.

METHODS

This study included 451 Chinese children with moderate to severe clinically unexplained DD/MR. The subtelomere-MLPA (multiplex ligation dependent probe amplification) and Affymetrix human SNP array 6.0 were used to determine the subtelomeric copy number variations. The exact size and the breakpoint of each identified aberration were well defined.

RESULTS

The submicroscopic subtelomeric aberrations were identified in 23 patients, with a detection rate of 5.1%. 16 patients had simple deletions, 2 had simple duplications and 5 with both deletions and duplications. The deletions involved 14 different subtelomeric regions (1p, 2p, 4p, 6p, 7p, 7q, 8p, 9p, 10p, 11q, 14q, 15q, 16p and 22q), and duplications involved 7 subtelomeric regions (3q, 4p, 6q, 7p, 8p, 12p and 22q). Of all the subtelomeric aberrations found in Chinese subjects, the most common was 4p16.3 deletion. The sizes of the deletions varied from 0.6 Mb to 12 Mb, with 5-143 genes inside. Duplicated regions were 0.26 Mb to 11 Mb, with 6-202 genes inside. In this study, four deleted subtelomeric regions and one duplicated region were smaller than any other previously reported, specifically the deletions in 11q25, 8p23.3, 7q36.3, 14q32.33, and the duplication in 22q13. Candidate genes inside each region were proposed.

CONCLUSIONS

Submicroscopic subtelomeric aberrations were detected in 5.1% of Chinese children with clinically unexplained DD/MR. Four deleted subtelomeric regions and one duplicated region found in this study were smaller than any previously reported, which will be helpful for further defining the candidate dosage sensitive gene associated with DD/MR.

Chromosomal microarray interpretation: what is a child neurologist to do?

The chromosomal microarray now plays a central role in the evaluation of children with neurologic developmental disorders, including global developmental delay, mental retardation, and increasingly also autistic spectrum disorders. As arrays become more sophisticated and their use more widespread, the child neurologist is likely to encounter abnormal chromosomal microarray results. The interpretation of such data is not always straightforward. This review article discusses in a practical manner the nature of chromosomal microarray results, describes an algorithm to help the child neurologist navigate a variety of testing scenarios, and proposes a standardized system for ranking array data based on levels of evidence of genotype-phenotype correlation.

Evidence-based medicine and practice guidelines: application to genetics

The Professional Practice and Guidelines Committee of the American College of Medical Genetics has the responsibility of overseeing the development of guidelines for the practice of clinical genetics. In the past, most, if not all, guidelines were primarily based on expert opinion. However, recently the goal has become to develop guidelines that are more evidence-based, or at least, to recognize the level of evidence available to the authors of these documents. This article reviews the challenges that are faced by geneticists who are charged with the development of practice guidelines.

1q44-qter trisomy: clinical report and review of the literature

Subtelomeric rearrangements are one of the main causes of multiple congenital anomalies and mental retardation, and they are detected in 5% of patients. We report on a 6.5-year-old boy with mental retardation, dysmorphic features, and behavioral problems, who revealed 1q44-qter trisomy and 22q13.3-qter monosomy due to a maternal cryptic translocation t(1;22). We compared the clinical and cytogenetic data of our patient with those of another case presenting a pure 22qter monosomy and with those of all 1qter trisomy cases reported in the international literature. To the best of our knowledge, the subterminal 1q trisomy found in the present case has been reported in only 12 patients to date (including five familial cases). This report aims to contribute to our understanding of 1q44-qter trisomy.

[Genetic diagnostic criteria in cases of mental retardation and development of idiopathic origin]

Different studies show that mental retardation affects 1-3% of the population, and in about 50 % of the cases the aetiology is unknown. The uncertainty on the aetiology, and recurrence, means that prevention of mental retardation can have serious, therapeutic, social, and even economic repercussions. The key is to obtain an accurate diagnosis, proving a clinical hypothesis by the accomplishment of the most suitable genetic tests. Due to the increasing development of the technology in the field of the genetics, and the availability of new tests, this article reviews the criteria established in the practice guidelines from different scientific societies (paediatric, neurological and genetic) with respect to their use in diagnosis and integrates them from the point of view of their use in mental retardation and developmental delay.

The clinical content of preconception care: genetics and genomics

The prevalence of paternal and maternal genetic conditions that affect pregnancy varies according to many factors that include parental age, medical history, and family history. Although some genetic conditions that affect pregnancy are identified easily early in life, other conditions are not and may require additional diagnostic testing. A complete 3-generation family medical history that includes ethnicity information about both sides of the family is arguably the single best genetic "test" that is applicable to preconception care. Assessment of genetic risk by an experienced professional has been shown to improve the detection rate of identifiable risk factors. Learning about possible genetic issues in the preconception period is ideal, because knowledge permits patients to make informed reproductive decisions. Options that are available to couples before conception include adoption, surrogacy, use of donor sperm, in vitro fertilization after preimplantation genetic diagnosis, and avoidance of pregnancy. Future technologic advances will increase the choices that are available to couples.

Application of array-based comparative genome hybridization in children with developmental delay or mental retardation

Children with developmental delay or mental retardation (DD/MR) are commonly encountered in child neurology clinics, and establishing an etiologic diagnosis is a challenge for child neurologists. Among the etiologies, chromosomal imbalance is one of the most important causes. However, many of these chromosomal imbalances are submicroscopic and cannot be detected by conventional cytogenetic methods. Microarray-based comparative genomic hybridization (array CGH) is considered to be superior in the investigation of chromosomal deletions or duplications in children with DD/MR, and has been demonstrated to improve the diagnostic detection rate for these small chromosomal abnormalities. Here, we review the recent studies of array CGH in the evaluation of patients with idiopathic DD/MR.

Oligonucleotide microarrays for clinical diagnosis of copy number variation

Detection of genomic copy number variation is now considered the standard of care in the evaluation of children with developmental delay, and is used for other clinical indications such as multiple congenital anomalies and autism spectrum disorders. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variation, but microarray based comparative genomic hybridization (array CGH) offers several advantages as an adjunct to traditional cytogenetic methods such as karyotype and FISH. This unit focuses on oligonucleotide arrays, but includes background information on basic differences between oligonucleotide arrays and bacterial artificial chromosome (BAC) arrays. Array sensitivity is influenced by probe coverage or density, probe location, and choice of oligo array formats (i.e., targeted versus whole genome). Array platform influences the likelihood of detecting variants of unknown significance. Clinical interpretation of such variants is discussed.

Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray

PURPOSE

Array comparative genomic hybridization is rapidly becoming an integral part of cytogenetic diagnostics. We report the design, validation, and clinical utility of an oligonucleotide array which combines genome-wide coverage with targeted enhancement at known clinically relevant regions.

METHODS

Probes were placed every 75 kb across the entire euchromatic genome to establish a chromosomal "backbone" with a resolution of approximately 500 kb, which is increased to approximately 50 kb in targeted regions.

RESULTS

For validation, 30 samples showed 100% concordance with previous G-banding and/or fluorescence in situ hybridization results. Prospective array analysis of 211 clinical samples identified 33 (15.6%) cases with clinically significant abnormalities. Of these, 23 (10.9%) were detected by the "targeted" coverage and 10 (4.7%) by the genome-wide coverage (average size of 3.7 Mb). All abnormalities were verified by fluorescence in situ hybridization, using commercially available or homebrew probes using the 32K bacterial artificial chromosome set. Four (1.9%) cases had previously reported imbalances of uncertain clinical significance. Five (2.4%) cases required parental studies for interpretation and all were benign familial variants.

CONCLUSIONS

Our results highlight the enhanced diagnostic utility of a genome-wide plus targeted array design, as the use of only a targeted array would have failed to detect 4.7% of the clinically relevant imbalances.

Monosomy 1p36 deletion syndrome

Monosomy 1p36 results from a heterozygous deletion of the most distal chromosomal band on the short arm of chromosome 1. Occurring in approximately 1 in 5,000 live births, monosomy 1p36 is the most common terminal deletion observed in humans. Monosomy 1p36 is associated with mental retardation, developmental delay, hearing impairment, seizures, growth impairment, hypotonia, and heart defects. The syndrome is also characterized by several distinct dysmorphic features, including large anterior fontanels, microcephaly, brachycephaly, deep-set eyes, flat nose and nasal bridge, and pointed chin. Several genes have been proposed as causative for individual features of the phenotype. In addition, based upon molecular characterization of subjects with monosomy 1p36, several mechanisms for the generation and stabilization of terminal deletions have been proposed.

Diagnostic utility of array-based comparative genomic hybridization in a clinical setting

Array-based comparative genomic hybridization is a recently introduced technique for the detection of submicroscopic genomic imbalances (deletions or duplications) across the entire genome. To assess the potential utility of a widely available array-based comparative genomic hybridization platform that targets specific, clinically relevant, loci across the genome for cytogenetic diagnosis in a clinical setting, we reviewed the medical records of all 373 patients at Children's Hospital Boston who had normal chromosomal analysis and were tested with this targeted array-based comparative genomic hybridization over a 1-year period from November 1, 2004 to October 31, 2005. These patients were tested because of a suspicion of chromosomal abnormalities based on their clinical presentation. Thirty-six patients (9.7%) had abnormal array-based comparative genomic hybridization results. Twenty patients (5.4%) had potentially pathogenetic genomic imbalances and 16 patients (4.3%) had copy number variations that are not believed to be pathogenetic. Thirteen of 234 patients (5.6%) with mental retardation/global developmental delay, 10/114 patients (8.8%) with facial dysmorphism, 5/58 patients (8.6%) with multiple congenital anomalies, and 4/35 patients (11.4%) with both facial dysmorphism and multiple congenital anomalies had potentially pathogenetic genomic imbalances. Targeted array-based comparative genomic hybridization is a clinically available test that is useful in the evaluation of patients suspected of having chromosomal disorders. However, it is best used as an adjunct to chromosomal analysis when a clear genetic diagnosis is unavailable.

The clinical utility of enhanced subtelomeric coverage in array CGH

Telomeric chromosome abnormalities are a substantial cause of mental retardation and birth defects. Although subtelomeric fluorescence in situ hybridization (FISH) probes have been widely used to identify submicroscopic telomeric rearrangements, array-based comparative genomic hybridization (array CGH) has emerged as a more efficient and comprehensive detection method. Due to the clinical relevance of telomeric abnormalities, it has been proposed that array CGH using panels of BAC clones that map to regularly spaced intervals along the length of each telomere could be used to characterize subtelomeric aberrations more precisely in a single experiment. We have added 1,120 FISH-mapped BAC clones to our microarray to enhance the coverage of the 41 unique human subtelomeric regions. Contigs of clones were selected in increments of approximately 0.5 Mb beginning with the most distal unique sequence for each subtelomere and extending on average approximately 5.7 Mb toward the centromere. We have used this microarray to characterize 169 clinically significant subtelomeric abnormalities identified out of nearly 7,000 consecutive clinical cases analyzed by array CGH in our diagnostic laboratory. The expanded telomere coverage was sufficient to define the breakpoints of over half (56%) of the chromosome abnormalities. However, 44% of the subtelomeric aberrations extended beyond the size of this expanded coverage suggesting that many subtelomeric abnormalities are >5 Mb in size and that greater representation may be of even more value. In addition to identifying 6 cases of complex rearrangements, we have identified 42 cases of interstitial deletions that would have been missed by subtelomere FISH panels that use a single clone to the most distal unique sequence for each region. Microarrays designed to investigate regions known to be involved in chromosome abnormalities will enhance the detection of cytogenetic abnormalities at unprecedented resolution and frequency.

Whole-genome array-CGH identifies novel contiguous gene deletions and duplications associated with developmental delay, mental retardation, and dysmorphic features

Cytogenetic imbalances are the most frequently identified cause of developmental delay or mental retardation, which affect 1-3% of children and are often seen in conjunction with growth retardation, dysmorphic features, and various congenital anomalies. A substantial number of patients with developmental delay or mental retardation are predicted to have cytogenetic imbalances, but conventional methods for identifying these imbalances yield positive results in only a small fraction of these patients. We used microarray-based comparative genomic hybridization (aCGH) to study a panel of 20 patients predicted to have chromosomal aberrations based on clinical presentation of developmental delay or mental retardation, growth delay, dysmorphic features, and/or congenital anomalies. Previous G-banded karyotypes and fluorescence in situ hybridization results were normal for all of these patients. Using both oligonucleotide-based and bacterial artificial chromosome (BAC)-based arrays on the same panel of patients, we identified 10 unique deletions and duplications ranging in size from 280 kb to 8.3 Mb. The whole-genome oligonucleotide arrays identified nearly twice as many imbalances as did the lower-resolution whole-genome BAC arrays. This has implications for using aCGH in a clinical setting. Analysis of parental DNA samples indicated that most of the imbalances had occurred de novo. Moreover, seven of the 10 imbalances represented novel disorders, adding to an increasing number of conditions caused by large-scale deletions or duplications. These results underscore the strength of high-resolution genomic arrays in diagnosing cases of unknown genetic etiology and suggest that contiguous genomic alterations are the underlying pathogenic cause of a significant number of cases of developmental delay.

Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs

Array-based comparative genomic hybridization is ushering in a new standard for analyzing the genome, overcoming the limits of resolution associated with conventional G-banded karyotyping. The first genomic arrays were based on bacterial artificial chromosome clones mapped during the initial phases of the Human Genome Project. These arrays essentially represented multiple fluorescence in situ hybridization assays performed simultaneously. The first arrays featured a targeted design, consisting of hundreds of bacterial artificial chromosome clones limited mostly to genomic regions of known medical significance. Then came whole-genome arrays, which contained bacterial artificial chromosome clones from across the entire genome. More recently, alternative designs based on oligonucleotide probes have been developed, and all these are high-density whole-genome arrays with resolutions between 3 and 35 kb. Certain clinical circumstances are well suited for investigation by targeted arrays, and there are others in which high-resolution whole-genome arrays are necessary. Here we review the differences between the two types of arrays and the clinical contexts for which they are best suited. As array-based comparative genomic hybridization is integrated into diagnostic laboratories and different array designs are used in appropriate clinical contexts, this novel technology will invariably alter the testing paradigm in medical genetics and will lead to the discovery of novel genetic conditions caused by chromosomal anomalies.

Linking family history in obstetric and pediatric care: assessing risk for genetic disease and birth defects

Family history captures the collective influence of shared genetic susceptibility, shared environmental factors, and common behaviors within families. Throughout the reproductive continuum, pediatricians, obstetricians, family practitioners, genetic counselors, and other clinicians can work with families to elicit relevant family history information and factor it into risk-assessment calculations and, when appropriate, decision-making. Current screening tools have focused on understanding the risk for single-gene disorders, chromosomal conditions, and teratogen exposures during the preconception, prenatal, and interconception periods. More research and data are needed to understand how family history influences risk for a wide variety of complex birth outcomes such as preterm birth, stillbirth, and many birth defects. With a better understanding of the impact of family history on many adverse birth outcomes, tools for the collection of a broader set of pertinent family history information must be developed.

Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation

The clinical implementation of array comparative genomic hybridization has revolutionized the diagnosis of patients with syndromic or nonsyndromic mental retardation. Multiple studies of hundreds of patients with idiopathic mental retardation, and normal karyotype and/or subtelomeric testing using genome-wide microarray platforms with approximately 2000 to >30,000 (tiling-path) interrogating BAC/PAC probes have detected chromosome abnormalities in up to 17% of cases. Surprisingly, some of the pathogenic changes are mosaic and not detectable in conventional karyotyping. Commercially available genome-wide microarrays with >300,000 synthesized oligonucleotide probes enable higher resolution and sensitivity and will probably replace the BAC/PAC arrays in clinical laboratories.

Cryptic telomere imbalance: A 15-year update

It has been 15 years since we proposed that assays of telomere integrity might reveal cryptic translocations and deletions as a significant cause of mental retardation (MR) in patients with normal G-banded karyotypes. Development of unique genomic probes adjacent to the subtelomeric repeats of each chromosome arm allowed multiplex FISH analyses that confirmed such cryptic telomeric imbalances in 3-6% of all unexplained MR. Although such "telomere FISH" analysis quickly became standard of care, limitations of this technology platform included a lack of information on the size and gene content of the deleted/duplicated segments and the failure to detect interstitial deletions not involving the most distal unique clone. The development of "molecular ruler" clone sets for every human telomere provided the foundation for accurate determination of size and gene content of each imbalance, as well as the detection of interstitial deletions within these regions. Array comparative genomic hybridization (aCGH) has emerged as a powerful technology to assess single copy changes (monosomy or trisomy) at targeted loci such as telomeres or across the whole genome. This technology now replaces multiplex FISH for the assessment of telomere integrity in unexplained MR and has the advantage of efficiently determining the size and gene content of the imbalance, as well as detecting interstitial deletions near telomeres or anywhere else in the genome covered by the array design. The application of aCGH in several studies of unexplained MR has confirmed that telomere imbalances are overrepresented compared to "average" chromosomal regions, although this is likely due to random chromosome breakage rather than specific molecular mechanisms associated with the genomic architecture of human telomeres. Telomere imbalances are significantly larger than initially envisioned ( approximately 40% are >5 Mb in size), and indicate the analytic sensitivity of the G-banded karyotype is much lower than previously thought. Finally, experience with smaller benign variants compared to larger pathogenic imbalances at telomeres serves as a model for approaching whole-genome aCGH in a clinical setting.

Nablus mask-like facial syndrome is caused by a microdeletion of 8q detected by array-based comparative genomic hybridization

In 2000, Teebi reported on a 4-year-old boy with a distinctive pattern of malformation, which he termed the "Nablus mask-like facial syndrome" (OMIM# 608156). Characterization of this syndrome has been difficult because of the paucity of patients described in the medical literature and its unknown etiology and pathogenesis. We present two patients with Nablus mask-like facial syndrome who both display a microdeletion in the 8q21-8q22 region detected by array-based comparative genomic hybridization. Patient 1, a boy, has a distinct facial appearance characterized by severe blepharophimosis, tight-appearing glistening facial skin, sparse and unruly hair, a flat and broad nose, and distinctive ears that are triangular in shape with prominent antihelices. He also demonstrates camptodactyly, contractures, unusual dentition, cryptorchidism, mild developmental delay, and a happy demeanor. Patient 2, a girl with a strikingly similar phenotype, was previously described in a report by Salpietro et al. 2003. She has distinctive ears, dental anomalies, and developmental delay. The etiology of her pattern of malformation was not identified at that time. Although high-resolution chromosome and subtelomeric FISH analyses were normal, array-based comparative genomic hybridization revealed an approximately 4 Mb deletion involving the 8q21.3-8q22.1 region in both patients. This region encompasses a number of genes that may contribute to this unique phenotype. These results demonstrate a chromosomal microdeletion as the etiology of Nablus mask-like facial syndrome and emphasize the diagnostic utility of array-based comparative genomic hybridization in the evaluation of multiple malformation syndromes of previously unrecognized causation.

Diagnostic yield of chromosome analysis in patients with developmental delay or mental retardation who are otherwise nondysmorphic

There is a standard recommendation that chromosomes be obtained in any patient who presents with developmental delay (DD) or mental retardation (MR) regardless of whether or not they have dysmorphic features. Increasingly, if patients are physically well-formed, the option to perform a karyotype is questioned because of the presumed low yield of a chromosomal abnormality. We hypothesize that patients with DD/MR who are non-dysmorphic do not have abnormal chromosomes at a rate high enough to warrant obtaining a karyotype on all patients in this population. A retrospective analysis of patients with DD/MR who were non-dysmorphic was performed. The total number of subjects was 134. Of these, 120 patients were recommended to have high-resolution chromosomes performed, among whom seven were lost to follow-up. In the remaining 113 patients, all had normal karyotypes. Three subjects were found to have fragile X syndrome, accounting for 3% of the males. One subject had a pathological mutation in MECP2. Our yield of chromosome analysis in non-dysmorphic patients with DD/MR is less than that previously described. The role of array-comparative genomic hybridization (array-CGH) as an auxiliary or alternative procedure in this patient population will be discussed.