Vaidehi Jobanputra

Copy-Number Disorders Are a Common Cause of Congenital Kidney Malformations

We examined the burden of large, rare, copy-number variants (CNVs) in 192 individuals with renal hypodysplasia (RHD) and replicated findings in 330 RHD cases from two independent cohorts. CNV distribution was significantly skewed toward larger gene-disrupting events in RHD cases compared to 4,733 ethnicity-matched controls (p = 4.8 × 10(-11)). This excess was attributable to known and novel (i.e., not present in any database or in the literature) genomic disorders. All together, 55/522 (10.5%) RHD cases harbored 34 distinct known genomic disorders, which were detected in only 0.2% of 13,839 population controls (p = 1.2 × 10(-58)). Another 32 (6.1%) RHD cases harbored large gene-disrupting CNVs that were absent from or extremely rare in the 13,839 population controls, identifying 38 potential novel or rare genomic disorders for this trait. Deletions at the HNF1B locus and the DiGeorge/velocardiofacial locus were most frequent. However, the majority of disorders were detected in a single individual. Genomic disorders were detected in 22.5% of individuals with multiple malformations and 14.5% of individuals with isolated urinary-tract defects; 14 individuals harbored two or more diagnostic or rare CNVs. Strikingly, the majority of the known CNV disorders detected in the RHD cohort have previous associations with developmental delay or neuropsychiatric diseases. Up to 16.6% of individuals with kidney malformations had a molecular diagnosis attributable to a copy-number disorder, suggesting kidney malformations as a sentinel manifestation of pathogenic genomic imbalances. A search for pathogenic CNVs should be considered in this population for the diagnosis of their specific genomic disorders and for the evaluation of the potential for developmental delay.

Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements

Purpose: To demonstrate the accuracy and sensitivity of Representational Oligonucleotide Microarray Analysis (ROMA) to describe copy number changes in patients with chromosomal abnormalities.Methods: ROMA was performed using BglII digested DNA from two cases with cytogenetically detected deletions and one case with an unbalanced terminal rearrangement detected only by subtelomeric FISH. Hybridization was to an 85,000-probe oligonucleotide microarray, providing an average resolution of 35 kb. FISH was used to confirm some of the ROMA findings.Results: By ROMA, a del(13)(q14.3q21.2) was shown to be noncontiguous, with deletions extending from 53.08 to 61.40 Mb and from 72.88 to 74.83 Mb. The 10-Mb deletion contained only six known genes. FISH confirmed the noncontiguous nature of the deletion, as well as a small amplification in 6q that was also found in the patients mother. A del(4)(q12q21.2) was found by ROMA to be 23 Mb in length, from 58.8 to 81.9 Mb on chromosome 4, in agreement with the cytogenetically assigned breakpoints. ROMA showed that an unbalanced “subtelomeric” rearrangement involved a 6-Mb deletion of 22q and an 8-Mb duplication of 16q.Conclusions: ROMA can define cytogenetic aberrations with extraordinary precision. Unexpected findings included the interrupted nature of the deletion in 13q and the large size of the imbalances in the “subtelomeric” rearrangement. Together with the information from the human genome sequence and proteomics, the ability to define rearrangements with “ultra-high” resolution will improve the ability to provide accurate prognosis both prenatally and postnatally to parents of offspring with chromosomal aberrations.

Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis

X-linked congenital generalized hypertrichosis (Online Mendelian Inheritance in Man 307150) is an extremely rare condition of hair overgrowth on different body sites. We previously reported linkage in a large Mexican family with X-linked congenital generalized hypertrichosis cosegregating with deafness and with dental and palate anomalies to Xq24-27. Using SNP oligonucleotide microarray analysis and whole-genome sequencing, we identified a 389-kb interchromosomal insertion at an extragenic palindrome site at Xq27.1 that completely cosegregates with the disease. Among the genes surrounding the insertion, we found that Fibroblast Growth Factor 13 (FGF13) mRNA levels were significantly reduced in affected individuals, and immunofluorescence staining revealed a striking decrease in FGF13 localization throughout the outer root sheath of affected hair follicles. Taken together, our findings suggest a role for FGF13 in hair follicle growth and in the hair cycle.

Indolent small intestinal CD4+ T-cell lymphoma is a distinct entity with unique biologic and clinical features.

Enteropathy-associated T-cell lymphomas (EATL) are rare and generally aggressive types of peripheral T-cell lymphomas. Rare cases of primary, small intestinal CD4+ T-cell lymphomas with indolent behavior have been described, but are not well characterized. We describe morphologic, phenotypic, genomic and clinical features of 3 cases of indolent primary small intestinal CD4+ T-cell lymphomas. All patients presented with diarrhea and weight loss and were diagnosed with celiac disease refractory to a gluten free diet at referring institutions. Small intestinal biopsies showed crypt hyperplasia, villous atrophy and a dense lamina propria infiltrate of small-sized CD4+ T-cells often with CD7 downregulation or loss. Gastric and colonic involvement was also detected (n = 2 each). Persistent, clonal TCRβ gene rearrangement products were detected at multiple sites. SNP array analysis showed relative genomic stability, early in disease course, and non-recurrent genetic abnormalities, but complex changes were seen at disease transformation (n = 1). Two patients are alive with persistent disease (4.6 and 2.5 years post-diagnosis), despite immunomodulatory therapy; one died due to bowel perforation related to large cell transformation 11 years post-diagnosis. Unique pathobiologic features warrant designation of indolent small intestinal CD4+ T-cell lymphoma as a distinct entity, greater awareness of which would avoid misdiagnosis as EATL or an inflammatory disorder, especially celiac disease.

Mutations in the Cholesterol Transporter Gene ABCA5 Are Associated with Excessive Hair Overgrowth

Inherited hypertrichoses are rare syndromes characterized by excessive hair growth that does not result from androgen stimulation, and are often associated with additional congenital abnormalities. In this study, we investigated the genetic defect in a case of autosomal recessive congenital generalized hypertrichosis terminalis (CGHT) (OMIM135400) using whole-exome sequencing. We identified a single base pair substitution in the 5′ donor splice site of intron 32 in the ABC lipid transporter gene ABCA5 that leads to aberrant splicing of the transcript and a decrease in protein levels throughout patient hair follicles. The homozygous recessive disruption of ABCA5 leads to reduced lysosome function, which results in an accumulation of autophagosomes, autophagosomal cargos as well as increased endolysosomal cholesterol in CGHT keratinocytes. In an unrelated sporadic case of CGHT, we identified a 1.3 Mb cryptic deletion of chr17q24.2-q24.3 encompassing ABCA5 and found that ABCA5 levels are dramatically reduced throughout patient hair follicles. Collectively, our findings support ABCA5 as a gene underlying the CGHT phenotype and suggest a novel, previously unrecognized role for this gene in regulating hair growth.

Using FISH to increase the yield and accuracy of karyotypes from spontaneous abortion specimens.

Cytogenetic analysis of spontaneous abortions is frequently complicated by culture failure and maternal cell contamination (MCC). The objective of the study is to demonstrate that multiplex fluorescence in situ hybridization (FISH) can increase the yield and accuracy of karyotypes from spontaneous abortion specimens.

Prenatal diagnosis of chromothripsis, with nine breaks characterized by karyotyping, FISH, microarray and whole‐genome sequencing

Detection of de novo complex chromosomal rearrangements (CCR) in prenatal testing is extremely rare. CCRs are defined as constitutional structural rearrangements involving three or more chromosomes or more than three breakpoints. A survey of 269,371 prenatal studies1 detected only 0.03% complex rearrangements out of 246 that were determined to be de novo. Recent whole-genome sequencing studies using large-insert jumping libraries have found that cryptic complexity, particularly cryptic inversions, often occurs at the breakpoints and in some cases can introduce a degree of complexity as significant as ‘chromothripsis’ to events that appear to be canonical rearrangements at karyotypic resolution2. The term chromothripsis was initially coined by Stephens et al.3 to explain the mechanism involved in massive chromosomal rearrangements in cancers. Once defined, the concept was widely adopted to help explain complex rearrangements in the germline 4,2. All reported chromothripsis rearrangements share several features in common, including: a) The occurrence of a single catastrophic genomic event resulting in chromosome shattering. The shattered pieces contain double stranded breaks that are reassembled into mosaic chromosomes. b) The reassembly of the majority of fragments of DNA in what appears to be random fashion with little sequence homology at the breakpoints. c) Unique to congenital chromothripsis, the lack of major duplications and deletions during reassembly. Most genomic changes detected in the germline are copy neutral or span only a few base pairs, lacking the frequent larger deletions and duplications observed in cancer chromothripsis. This is likely due to selection in these cases for fetal viability. There is also growing evidence that chromothripsis occurs mainly in spermatogenesis. For reviews, see Kloosterman et. al. 20114, 20125, 20136 and Pellestor, 20147. We report a prenatal case initially diagnosed by karyotyping as a CCR with 6 breakpoints, 5 chromosomes involved in a four-way translocation and a separate two-way translocation. The p and q arms of the same chromosome 18 were involved in distinct translocations. Further analysis by whole-genome sequencing showed that two of the breakpoints were more complex than seen by karyotype, giving a total of 9 breakpoints in 5 chromosomes. Small < 1000 bp deletions or duplications were detected at these breakpoints, which interrupted 7 genes. We believe this case fits the criteria for chromothripsis. A 28 year old woman in her first pregnancy presented for amniocentesis sampling at 21 weeks gestation. Ultrasound and MRI revealed bilateral ventriculomegaly (13mm and 15mm) and colpocephaly, with partial agenesis of the corpus callosum. The prior family history was unremarkable with no unusual environmental exposures known to the mother or father upon questioning. The initial FISH analysis with AneuVysion (Abbott), suggested a normal female. However, the pregnancy was terminated at 22 weeks due to the ultrasound findings. Cytogenetic and FISH analysis with telomere probes on amniocytes harvested post termination revealed a 46,XX,t(3;18;5;7)(p25;p11.2;q13.3;q32),t(9;18)(p22;q21) karyotype in all cells examined. SNP oligonucleotide microarray analysis (Affymetrix Cytoscan HD) on fetal DNA showed no loss or gain of chromosomal material at any of the breakpoints. This unusual complex karyotype was confirmed in fetal kidney cells. Chromosomes from both parents were normal. Fetal genomic DNA was accessioned in the Developmental Genome Anatomy Project as case DGAP259. Next generation sequencing of fetal genomic DNA using large-insert jumping libraries at ~3 kb resolution, followed by PCR and Sanger validation, resolved 5 of the putative breaks. In addition to the 6 visible breakpoints, a 184.5kb cryptic inversion at the chr3/chr18 junction on the p arm of the derivative 18 was identified and the sixth break point on the derivative 5 was found to be more complex, involving the insertion of small portions of chromosomes 3 and 7 at the chr5/chr18 junction (Figure 1). The breakpoints were refined to 3p24.3, 3p26.3; 5q14.3; 7q35, 7q36.3 and inv(18p11.31p11.31). The formula for the 4 chromosome translocation was thus revised as: t(3;18;5;7)(7qtel→7q36.3::3p24.3→3qter;3pter→3p26.3::18p11.31p11.31::18p11.31→18q2 1.31::9p23→9qter;5pter→5q14.3::7q35→7q36.3::3p24.3→3p26.3::18p11.31→18pter;7pter →7q35::5q14.3-5qter). The two-chromosome translocation was rewritten as t(9;18)(p23;q21.31). Figure 1 A. G-banded karyotype from kidney culture of the terminated fetus. Arrows indicate the 6 visible breakpoints. B. Diagram of the complex rearrangement after information from whole genome sequencing. The arrows indicate areas of complexity in 19p and 5q ... Using the new nomenclature for sequenced breakpoints proposed by Ordulu et al.8, this would be written as: “46,XX,t(3;18;5;7)(p25;p11.2;q13.3;q32),t(9;18)(p22;q21)dn.seq[GRCh37/hg19](3,5,7,9,18)cx,der(3)(7qter->7q36.3(155,701,797)::3p24.3(17,392,144)->3qter) dn,der(5)(5pter->5q14.3(88,756,2{48-56})::7q35q36.3(147,718,91{1-9}-155,700,873)::AGAAC::3p24.3p26.3(17,392,136-1,408,99{6})::18p11.31(6,375,05{1})->1 8pter)dn,der(7)(7pter->7q35(147,718,90{7-8})::5q14.3(88,756,2{39-40})->5qte r)dn,der(9)(18qter->18q21.31(54,660,13{8})::9p23(9,646,47{5})->9qter)dn,der (18)(3pter->3p26.3(1,408,984)::18p11.31(6,559,611-6,375,0{52-48})::18p11.31 q21.31(6,559,{598-602}-54,660,136)::9p23(9,646,471)->9pter)dn” Seven OMIM annotated genes were disrupted at the breakpoints, with small base pair losses or gains in all 7 genes (Figure 2). On chromosome 3, CNTN6 (a neuronal membrane protein that functions as a cell adhesion molecule, believed to play a role in the development of the nervous system) and TBC1D5 (acts as a GTPase-activating protein for Rab family protein(s)) are interrupted. On chromosome 7, CNTNAP2 (a member of the neurexin family that acts as a cell adhesion molecule in the vertebrate nervous system and is implicated in numerous neurodevelopmental disorders) is disrupted. On chromosome 9, PTPRD (a signaling molecule regulating cell growth and development is disrupted. On chromosome 18, L3MBTL4 (a conserved gene down regulated or mutated in tumors, LOC100130480 (uncharacterized) and WDR7 (a gene possibly involved in cell cycle progression and gene regulation) are disrupted. The chromosome 5 breakpoint does not involve any gene disruption but does contain a gain of 18 bp. The 7q36.3 breakpoint does not involve a gene but resulted in a loss of 923 bp. This brings the total number of breaks in this chromosome complement to 9. Figure 2 Reassembly of all chromosomal regions that were involved in the translocations, according to HG19 (www.genome.ucsc.edu). At each breakpoint interrupted genes are shown above and bps of gain or deletion are shown below. The gains and losses were all well ... In our case the pregnancy was terminated because of the ultrasound abnormalities: a complete fetal autopsy was performed, which showed a very small brain for gestation (40 gm. vs. normal 75 gm.), the ventriculomegaly seen on fetal MRI, and an absent left kidney and small right kidney. The corpus callosum could not be visualized. All other structures were unremarkable. In the absence of USG detected anomalies, it will be very difficult to provide a risk for developmental abnormalities when chromothripsis is detected prenatally. Most reported cases with clinical data have been detected postnatally as apparently balanced rearrangements in patients with developmental delay. The spectrum of phenotype in individuals with chromothripsis “balanced” at the array level is yet to be determined, but will presumably reflect the nature of the disrupted genes. Chromothripsis seen prenatally is unlikely to contain major imbalances because of in utero selection for survival to the time of diagnosis. The characterization of this extremely complex abnormality illustrates the necessity of both cytogenetic and molecular testing. Chiang et al.2 sequenced 141 breakpoints from what were originally classified as cytogenetically balanced rearrangements and found that 19.2% of these fit the criteria for CCRs, a much higher percentage than previously believed1. The number of congenital cases showing chromothripsis suggests that all de novo balanced rearrangements detected prenatally by karyotyping in cases with ultrasound abnormalities should ideally be further analyzed by sequencing to determine possible undetected genetic changes. It is ironic that as molecular testing is becoming extremely sophisticated, chromosomal analysis is at present the only reliable method to initially detect rearrangements that would fit the criteria for chromothripsis.

Whole-Exome Sequencing in Adults With Chronic Kidney Disease: A Pilot Study

Chronic kidney disease (CKD) affects an estimated 14% of Americans (1, 2). These persons have 10- to 15-fold higher morbidity and mortality rates than the general population (1, 3). In most patients with CKD, the diagnosis is based on standard office work-up and sometimes kidney biopsy findings. However, early-stage CKD is often clinically silent, and subtypes can be difficult to distinguish on the basis of clinical data alone. Thus, in many persons, the precise cause of kidney failure remains unknown. Approximately 10% to 25% of patients with CKD note a family history of nephropathy (46), suggesting that in many cases the disease has a hereditary component. Recent advances in genomic technologies, such as chromosomal microarray and massively parallel (next-generation) sequencing, enable genome-wide analysis at a modest cost and precise definition of the molecular cause of many complex diseases (713). Application of these methods has suggested opportunities for individualized diagnosis and risk stratification, including targeted work-up and surveillance for associated disease complications (1113) and sometimes precision therapy (1215). However, studies to date have focused mainly on a limited range of disorders in pediatric cohorts or on cancer in adults (717); thus, the clinical utility of these approaches for a broader spectrum of diseases, particularly among adults, remains unclear. Applying chromosomal microarray analysis, we recently showed that 7.4% of 419 children with various forms of CKD had a major known pathogenic genomic imbalance that was not suspected after clinical assessment (18). These disorders were evenly distributed among patients clinically diagnosed with congenital and noncongenital forms of CKD, indicating that genetic analysis has utility across broad clinical categories. In most of these cases, the genetic findings either reclassified the disease or provided information that could guide subsequent clinical care, such as evaluation for metabolic or neuropsychiatric disease. Similarly, next-generation sequencing has been shown to have great utility for diagnosing genetic forms of nephrotic syndrome or congenital kidney defects in pediatric populations, albeit mainly in the context of targeted panels (1921). Whole-exome sequencing (WES) is a genome-wide testing approach that allows selective sequencing of the protein-coding regions of the genome, which are enriched for disease-associated variants (1215). Because of its genome-wide coverage, WES enables screening of most genes associated with kidney disease and can therefore be applied across diverse categories of renal disorders. Moreover, it can potentially identify novel etiologic genes for nephropathy or detect actionable incidental mutations unrelated to the primary indications for testing. For these reasons, WES is emerging as a preferred diagnostic tool for hereditary disorders (1215, 22, 23). In pediatric cohorts, WES recently identified diagnostic mutations in up to 11.5% of patients with congenital kidney anomalies and 26% of patients with steroid-resistant nephrotic syndrome, supporting its diagnostic utility for early-onset CKD (24, 25). However, the value of this sequencing method for the diagnosis and management of CKD in adults has not been adequately studied. We did a pilot study to test the utility of WES in adults referred for evaluation of CKD or hypertension. Methods Study Design The results of WES in a convenience sample of patients referred for evaluation of CKD were reviewed for their potential to inform clinical practice. To facilitate diagnostic interpretation of WES data, we compiled a list of genes encompassing most common Mendelian forms of kidney and hypertensive disorders. We next annotated the exomes for diagnostic variants in nephropathy genes and then analyzed other genes, including those recommended by the American College of Medical Genetics (ACMG), for return of medically actionable incidental findings (26). Patient Population and Setting The study sample was selected from a group of 344 patients seen at outpatient nephrology clinics between October 2013 and May 2014 at Columbia University Medical Center, a tertiary care medical center with a nephrology division offering highly specialized care for glomerular disorders. These 344 patients were referred for evaluation and management of kidney disease and consented to a general genetic research and biobanking protocol. Supplement Table 1 presents the characteristics of these 344 patients. From this group, we selected 81 adult patients (aged >18 years) (Supplement Table 2) for WES who fulfilled 1 of the following inclusion criteria: a family history of kidney disease (defined as any family member with urinary abnormalities or impaired kidney function, as reported by the patient), undiagnosed kidney disease, or clinical suspicion of a genetic kidney disease (for example, in a proband with young age of onset and no family history of nephropathy). The PKD1 gene is not well-captured by WES because of gene duplication (27), so patients fulfilling clinical diagnostic criteria for autosomal dominant polycystic kidney disease were not included in the WES study. Supplement. Supplementary Tables In addition to these 81 patients from Columbia University Medical Center, we also included 11 patients referred for suspected inherited kidney disease or hypertension from outside institutions. Three patients with familial tubulointerstitial nephropathy and 1 with early-onset hypertension were referred from 3 local practices in the United States (New York University and nephrology practices in suburban New York and Delaware). Four were referred for evaluation of Mendelian hypertension from the Polish Kidney Genetics Network (POLYGENES, www.polygenes.org), centered in the Department of Genetics at Pozna University of Medical Sciences and The Center of Medical Genetics GENESIS (Pozna, Poland). Three other patients were referred from Gaslini Institute (Genova, Italy) for evaluation of glomerulonephritis with nondiagnostic kidney biopsies. All participants gave informed consent, and the study was approved by the Columbia University Institutional Review Board and local ethics committees. WES and Sequence Interpretation Staff extracted DNA from whole blood. Telomere length was measured using genomic DNA from whole blood, as previously described (28, 29). For WES, fragment libraries using 200 ng of genomic DNA were constructed from each sample, following the Agilent standard library preparation protocol for TruSeq (Illumina). Exome capture was done with the SureSelectXT Human All Exon V4 (51 Mb) kit (Agilent), and sequencing was done using the HiSeq 2000 or 2500 (Illumina) at the Columbia Genome Center. On average, 92.83 million independent paired-end reads (18.56-Gb bases) were generated per sample to provide an average coverage of 110-fold, with 99.17% of target regions being covered at least 10-fold. The paired-end reads (read size, 101 bp) were mapped to the human reference genome National Center for Biotechnology Information build 37 using BurrowsWheeler Aligner, version 0.5.9. The Genome Analysis Toolkit, version 1.6-13, was used to call germline single nucleotide variants and insertions or deletions (indels). Variants were annotated for predicted effect on protein function (using ANNOVAR and SnpEff); allele frequency in public databases (ExAC, dbSNP, and the 1000 Genomes Project); and predicted pathogenicity with in silico algorithms, including PolyPhen and Combined Annotation Dependent Depletion scores (3036). Evidence for disease causality was assessed using ClinVar and the Human Genome Mutation Database (Qiagen), followed by manual review of the cited primary literature (33, 36). In addition, we developed a curated priority list of 287 Online Mendelian Inheritance in Man (OMIM; http://omim.org) genes implicated in Mendelian forms of kidney disorders and hypertension to facilitate clinical annotation (hereon, we refer to this gene list as nephropathy genes; see Supplement Table 3. A known limitation of exome sequencing is that some segments of the genome are not amenable to capture (23). Among the 287 nephropathy genes, 29 were identified with at least 1 exon that is not captured by the Agilent kit, representing potential blind spots in the analysis (Supplement Table 3). Variant interpretation was done by a panel of nephrologists or molecular geneticists with domain expertise in inherited kidney diseases (K.K., S.S.C., C.A., L.R., E.G., and A.G.G.), bioinformaticians (S.L. and D.A.F.), and a clinical molecular geneticist (V.J.), using the ACMG guidelines for clinical sequence interpretation (37). Detailed classification criteria for pathogenic and likely pathogenic variants are in Supplement Table 4. We also reviewed potentially pathogenic mutations in OMIM genes associated with other heritable disorders and in the ACMGs 59 actionable genes (26). All diagnostic variants were confirmed by Sanger sequencing. Finally, we verified the distribution of potentially functional variants in nephropathy genes in each exome. These potentially functional variants were defined as missense, nonsense, splice site, or indel variants with a minor allele frequency less than 1% in ExAC (a database of genetic variation in >60000 persons) and a Combined Annotation Dependent Depletion score greater than 10 (indicating a variant score in the top 10% of deleteriousness in a large reference data set of variants). We also verified allele frequencies using an anonymized in-house control data set derived from 9012 persons who had undergone WES for indications other than nephropathy; these control data included healthy parents of children with a developmental disorder and participants from genetic studies of amyotrophic lateral sclerosis or seizure disorders. Role of the Funding Source The study was funded by the New York State Empire Clinical Research Investigator Program, the Renal Research Institut

Bohring-Opitz syndrome (BOS) with a new ASXL1 pathogenic variant: Review of the most prevalent molecular and phenotypic features of the syndrome.

Bohring–Opitz syndrome (BOS) was first described by Bohring et al. [1999]. The authors reported four cases which had several features in common, including a prominent metopic suture, hypertelorism, exophthalmos, cleft lip and palate, limb anomalies, as well as difficulty feeding with severe developmental delays. In almost 50% of cases that meet the clinical criteria for BOS, de novo frameshift and nonsense mutations in the ASXL1 gene have been detected, suggesting that loss of function of this gene is a major cause. We report on the clinical characterization of one young female patient who was evaluated because of severe developmental delays, failure to thrive, and multiple minor anomalies and was clinically diagnosed with BOS. Whole exome sequencing analysis detected one novel disruptive frameshift mutation in the ASXL1 gene and we were also able to confirm the presence of two CFTR mutations associated with her chronic pancreatitis with acute severe breakthrough attacks requiring multiple ICU admissions. This latter complication of pancreatitis further contributed to the complexity of the clinical presentation and represents an independent genetic finding. Our case report emphasizes the importance of highly specific phenotypic characterization of patients with complex phenotypes before proceeding with molecular studies. That approach will lead to more accurate molecular data interpretation and better clinical genetic diagnosis, particularly for those patients with rare, difficult‐to‐diagnose disorders.

Prenatal PAH Exposure is Associated with Chromosome-specific Aberrations in Cord Blood

Chromosomal aberrations are associated with increased cancer risk in adults. Previously, we demonstrated that stable aberrations involving chromosomes 1-6 in cord blood are associated with prenatal exposure to polycyclic aromatic hydrocarbons (PAHs) measured in air and are disproportionate to genomic content. We now examine whether the association with air PAHs is chromosome-specific and extends to smaller chromosomes. Using whole chromosome paints for chromosomes 1-6, 11, 12, 14 and 19, and a 6q sub-telomere specific probe, we scored 48 cord bloods (1500 metaphases per sample) from newborns monitored prenatally for airborne PAH exposure in the Columbia Center for Childrens Environmental Health cohort. Frequencies of stable aberrations were calculated as incident aberrations per 100 cell equivalents scored, and examined for association with airborne PAHs. Aberrations in chromosome 6 occurred more frequently than predicted by genomic content (p<0.008). Levels of both prenatal airborne PAHs and stable aberration frequency in chromosomes 1-6 decreased to half the levels reported previously in the same cohort (mean PAH decreased from 3.6 to 1.8ng/m(3); mean stable aberration frequency from 0.56 to 0.24, SD=0.19). The mean stable aberration frequency was 0.45 (SD=0.15) in chromosomes 11-19. After adjusting for gender, ethnicity, and household smokers, the mean stable aberration frequency increased with increasing PAH exposure: with a doubling of prenatal PAH exposure, the mean stable aberration frequency for the chromosome1-6 group increased by a factor of 1.49 (95% CI: 0.84, 2.66; p=0.17); for chromosomes 11-19 mean stable aberration frequency increased by 2.00 (95% CI: 1.11, 3.62; p=0.02); for chromosome 6 alone, it increased by 3.16 (95% CI: 0.93, 10.77; p=0.06); there was no increase for chromosomes 1-5 (p>0.8). Aberrations in chromosomes 11, 12, 14, 19 and 6 were associated with prenatal exposure to PAHs in air, even at lower levels of PAH in air. The observed chromosome-specific effects of prenatal airborne PAHs raise concern about potential cancer risk.