Conceived and designed the experiments: MTL SH DJL. Performed the experiments: MTL SH STC SY LM JFL. Analyzed the data: MTL SH DJL JFL. Contributed reagents/materials/analysis tools: CAS SHK SWC. Wrote the paper: MTL.
The authors have declared that no competing interests exist.
Disorders of sexual development (DSD), ranging in severity from genital abnormalities to complete sex reversal, are among the most common human birth defects with incidence rates reaching almost 3%. Although causative alterations in key genes controlling gonad development have been identified, the majority of DSD cases remain unexplained. To improve the diagnosis, we screened 116 children born with idiopathic DSD using a clinically validated array-based comparative genomic hybridization platform. 8951 controls without urogenital defects were used to compare with our cohort of affected patients. Clinically relevant imbalances were found in 21.5% of the analyzed patients. Most anomalies (74.2%) evaded detection by the routinely ordered karyotype and were scattered across the genome in gene-enriched subtelomeric loci. Among these defects, confirmed
The acquisition of a sexual phenotype depends on critical embryonic steps, which initially commit the bipotential gonad to either a testis or an ovary and direct normal morphogenesis of external genitalia. Disruption of these developmental processes occurs frequently in humans as reflected by the high prevalence in newborns of disorders of sexual development (DSD) ranging in severity from genital abnormalities to complete sex reversal. Failure of testis descent or cryptorchidism is found in 2% of full-term males
The finding that several common syndromes (including mental retardation, developmental delay and autism) are caused by specific submicroscopic chromosomal rearrangements, opened up new avenues for dissecting complex human phenotypes
Cryptic chromosomal rearrangements are involved in the etiology of human reproductive disorders since Y chromosome microdeletions are associated with human male infertility. Based on this, we tested the hypothesis that submicroscopic chromosomal alterations, too small to be detected by routine cytogenetic methods, may exist in patients with human disorders of sexual development. We studied probands presenting with hypospadias, cryptorchidism and ambiguous genitalia, the most common genital defects seen in pediatric urology clinics. We compared the resolution of clinical detection of such cryptic abnormalities by microarray-based chromosomal screening and by the routinely used karyotype. We further analyzed the contribution of these structural anomalies to the observed GU phenotypes by studying their association with the genital traits, as well as their inheritance and their recurrence. For the first time, findings revealed the presence of frequent microdeletions and microduplications in the genome of children born with urogenital disorders and established
This study was approved by the Institutional Review Board Committee at the Baylor College of Medicine, Houston TX. Probands affected with unexplained syndromic and non-syndromic congenital genitourinary disorders including hypospadias, cryptorchidism or ambiguous genitalia were enrolled through Texas Children's Hospital and Ben Taub General Hospital, Houston TX. Known causes of these birth defects such as anomalies in the synthesis of testosterone or adrenal steroid hormones or exogenous modifiers were ruled out after examination by pediatric urologists or neonatologists. Written informed consents were obtained for infant/child subjects and from their parents. Blood was collected from the children during surgery for correction of the GU defects. Parents provided saliva specimens. Based on the novel CMA findings, additional cases were then identified through an existing database from Kleberg Cytogenetics Laboratory (Baylor College of Medicine, Houston TX). These additional probands were referred patients, mostly presenting with external genital ambiguity with or without subclinical phenotypes. Clinical indications at the time of the referral were taken from crude clinical comments on laboratory requisitions.
High molecular weight genomic DNA isolated from peripheral blood or saliva was submitted for chromosomal microarray analysis (CMA) to the Clinical Cytogenetics Laboratory at Baylor College of Medicine. CMA is a clinically validated targeted CGH array that covers over 150 distinct human clinically relevant chromosomal loci
All data are MIAME compliant and have been deposited in a MIAME compliant database.
Clinically significant CNVs included detection of well-characterized deletion/duplication syndromes, deletion/duplication >3 Mb in size or cytogenetically visible, and
FISH analysis was used to validate selected CMA findings >150 Kb in size, using the standard clinical cytogenetics laboratory protocol
Quantitative TaqMan copy number variant (CNV) assays (Applied Biosystems) were used as an alternate secondary confirmation to FISH analysis. All reactions with TaqMan CNV assays were performed in triplicate using the FAM dye label-based assay for the target of interest and the VIC dye label-based TaqMan CNV RNaseP for the internal controls. The targets were custom designed in the areas where most significant changes in the probes were detected. QPCR was performed with 20 ng gDNA according to the manufacturer's protocol in an Applied Biosystems One Step Plus Real-Time PCR System using the default universal cycling conditions. Relative quantitation analysis was done to estimate copy number for each sample by using the Copy Caller Software V1.0 (Applied Biosystems).
Metaphase preparations from PHA-stimulated patient lymphocyte cultures followed a standard protocol to obtain chromosomes at ≥600–50-band level
To analyze the frequency of
High molecular weight genomic DNA was isolated from peripheral blood of 116 children presenting with unexplained cases of disorders of sexual development ranging in severity from penile growth or testicular descent anomalies to genitalia ambiguity or complete sex reversal. Since the primary goal of this study was to improve the diagnosis of these urogenital defects and rapidly translate the findings to the clinic, DNA was analyzed using an established CGH microarray platform available for clinical diagnosis (chromosome microarray assay, CMA)
Chromosomal imbalances were detected in 37 (31.9%) of the 116 patients analyzed (
On the right, CMA detected imbalances were shown for each clinical condition (asterisks). To gain insight into the genomic distribution of the identified imbalances, all published single gene mutations associated with cryptorchidism (blue), hypospadias (green) and ambiguous genitalia (red) were reviewed and indicated on the left side of the chromosomes. References are available upon request.
No Aberration | Chromosomal Aberrations | Total | Rate of Detection of Non-Poly morphic CNV (%) | Rate of Detection of Clinically Significant CNV (%) | |||
Normal | Benign CNV | Non-Polymorphic CNV | |||||
Clinically Significant | UCS | ||||||
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Isolated cases | 21 | 3 | 11 | 1 | 36 | 33.3 | 27.8 |
Associated with other anomalies | 18 | 1 | 4 | 1 | 24 | 20.8 | 16.0 |
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Isolated cases | 12 | 0 | 3 | 2 | 17 | 29.4 | 17.7 |
Associated with other anomalies | 8 | 1 | 2 | 1 | 12 | 25.0 | 16.7 |
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Isolated cases | 15 | 0 | 2 | 0 | 17 | 11.8 | 11.8 |
Associated with other anomalies | 5 | 1 | 3 | 1 | 10 | 40.0 | 30.0 |
Total |
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Footnote: UCS: Uncertain Clinical Significance.
Locus | Case | GU defects | Associated anomalies | Concurrent G-banded karyotype | Array Platform | CNV(Signifi-cance) | Rearrangements seen in CMA | Min. size (Mb) | Secondary FISH | Min. genes | Inheritance |
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#1 | Cloacal Exstrophy, Prominent Labioscrotal Folds, No Apparent Genital Tubercle | Midline Defect, imperforate Anus, Left Foot Anomaly | 46, XX | CMA (Oligo V6.3) | Loss (P) | arr cgh 1p36.33(RP11-671C15->RP11-547D24)x1 | 1.25 | ish del(1)(p36.33p36.33)(RP11-465B22-)dn | 65 | De Novo |
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#6 | Ambiguous Genitalia (Referral) | None | 46,XY,der(5)(qter->q34::p14->qter) | CMA (Oligo V6.2) | Loss (P) | arr cgh 5p15.33p14.2(RP11-487N22->RP11-91L13)x1, 16p13(RP11-349E19)x1 | 24 | n/a | 145 | Unavailable |
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#12 | Gonadal Dysgenesis | None | 46,XY,der(9)del(9)(p23)dup(9)(p23p12) | CMA (Oligo V6.2) | Loss (P) | arr cgh 9p23p24.3(RP11-19G1->RP11-165F24)X1, 9p13.1p23(CTD-2349C9->RP11-3L8)X3 | 9.7 Mb in 9p23p24.3 and 26 Mb in 9p13.1p23 | ish der(9)(RP11-31F19-,RP11-381H12++,CTD-2349C9++) | 66 deleted and 285 duplicated | De Novo |
#13 | Gonadal Dysgenesis | None | 46,XY,der(9)del(9)(p24pter)dup(9)(p23p12) | CMA (V.5.0) | Loss (P) | arr cgh 9p24.1-pter(GS-43N6-RP11-165F24->RP11-146B14)X1 | 6.7 | n/a | 58 | De Novo | |
#9 | Swyer Syndrome | None | 46,XY,del(9)(p23) | CMA (V.5.0) | Loss (P) | arr cgh 9p24.3 (RP11-165F24->RP11-31F19)X1, 7p22.3(RP11-90P13->RP1-164D18 16D1S)X3 | 0.26 | n/a | 4 | Unavailable | |
#14 | Gonadal Dysgenesis | None | 46,XY,var(Y)(q12) | CMA (Oligo V6.3) | Loss (P) | arr cgh 9p23(RP11-19G1)x1 | 0.20 | ish del(9)(p23p23)(RP11-19G1dim) | 1 | Unavailable | |
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#15 | Ambiguous Genitalia (Referral) | Multiple Congenital Anomalies | XY t(12;15), del10q | CMA (V.5.0) | Loss (P) | arr cgh 10q26.1q26.3 (RP11-338O1->RP11-426G8)x1 | 57.4 | n/a | 620 | Unavailable |
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#22 | Ambiguous Genitalia (Referral) | None | 46,XY | CMA (V.5.0) | Loss (P) | arr cgh 19q12q13.11(RP11-142B21->RP11-618P17)x1 | 5.7 | Interstitial deletion between band 19q12 to 19q13.2 by partial karyotype | 49 | De Novo |
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#24 | Ambiguous Genitalia (Referral) | Developmental Delay | 46,XX,t(2;9)(p25.3;p22.1) | CMA (V.5.0) | Gain (P) | arr cgh 22q11.21(RP11-186O8->RP11-165F18)x3 | 1.6 | ish dup(22)(q11.2q11.2)(RP11-165F18x3) | 69 | Unavailable |
#25 | Smith-Lemli-Opitz Syndrome | None | n/a | CMA (V.5.0) | Loss (P) | arr cgh 22q11.21(RP11-186O8->RP11-165F18)x1 | 1.6 | ish del(22)(q11.2q11.2)(F5-) | 69 | Unavailable | |
#26 | Ambiguous Genitalia (Referral) | Wilms Tumor Tetralogy of Fallot, Developmental Delay, Mental Retardation | 46,XX,del(22)(q11.21q11.23) | CMA (V.5.0) | Loss (P) | arr cgh 22q11.2(RP11-186O8->RP11-165F18)x1 | 1.6 | ish del(22)(q11.2q11.2)(RP11-165F18-) | 69 | Unavailable | |
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#27 | Mixed Gonadal Dysgenesis | None | 45,X |
CMA (Oligo V6.2) | Loss (P)/Mosaic | Deletion in Yp11.31q11.22: Mos Turner arr cgh Y(RP11-112L19->RP11-223K9)x0 | 18.7 | n/a | 189 | Unavailable |
#28 | Mixed Gonadal Dysgenesis | None | n/a | CMA (Oligo V6.3) | Loss (P)/Mosaic | Deletion in Yp11.31q11.22: Mos Turner arr cgh Yp11.31q11.22(RP11-400O10->RP11-223K9)x1 | 18.8 | Retrospective: nuc ish Xcen(DXZ1x1),Ycen(DYZ3x0)[88]/Xcen(DXZ1x1),Ycen(DYZ3x1)[112] | 192 | Unavailable | |
#29 | Ambiguous Genitalia (Referral) | None | 46,X,add(X)(p22.3) | CMA (V.6.1) | Gain (P)/Mosaic | Presence of Yp11.31p11.2: arr cgh Yp11.31p11.2(RP11-112L19->RP11-418M8)x1 | 6 Mb of Yp on distal short arm of Chr. X | Retrospective: ish der(X)(CEP X+,LSI SRY+) | 44 | Unavailable | |
#30 | Gonadal Dysgenesis | None | n/a | CMA (V.6.1) | Gain (P)/Mosaic | Duplication in Yp11.31q11.21: arr cgh Yp11.31q11.21(RP11-112L19->RP11-460B21)x2 | 10.7 | Retrospective: ish Yp11.31(SRY-) |
116 | Unavailable |
Locus | Case | GU defects | Associated anomalies | Concurrent G-banded karyotype | Array platform | CNV(Signifi-cance) | Rearrangements seen in CMA | Min. size (Mb) | Secondary FISH | Min. genes | Inheritance |
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#7 | Cryptorchidism (inguinal) | None | 46, XY | CMA (Oligo V6.3) | Gain (P) | arr cgh 5p15.2(RP11-327L20)x3 | 0.1 | n/a, * | 1-8 | Present in maternal |
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#16 | Cryptorchidism (abdominal) | VACTERL Syndrome, imperforate Anus, Unilateral Renal Agenesis | n/a | CMA (Oligo V6.3) | Gain (P) | arr cgh 10p14 (RP11-796C22)x3 | 0.064 | FISH: ish dup(10)(p14)(RP11-590M7x3) | 3 | De Novo |
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#18 | Cryptorchidism (inguinal) | Transposition of Great Vessels, Ventricular Septal Defect, Developmental Delay, Epilepsy, Hypotonia | 46,XY,dup(12)(q24.2q24.31) | CMA (Oligo V6.3) | 2 Gains (one UCS and one P) | arr cgh 12q24.13 (RP3-329E11, RP1-66E7)x3, 12q24.21q24.31(RP11-902D13-RP11-197N18)x3 | 2 gains (12q24.13>116Kb; 12q24.21-12q24.3>7.9Mb) | n/a | 3 for 12q24.13 - 107 for 12q24.21q24.31 | Unavailable |
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#19 | Cryptorchidism | None | n/a | CMA (Oligo V6.2) | Loss (P) | arr cgh 15q11.2q12(RP11-289D12—>RP11-345N11)x1 | 3.9 | n/a | 126 | Unavailable |
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#33 | Cryptorchidism (abdominal) | Congenital Diaphragmatic Hernia | 46, XY | CMA (Oligo V6.3) | Gain (P) | arr cgh Xq28 (RP11-479B17)x3 | 0.159 | ish dup(X)(q28)(RP11-479B17x3) | 1 | De Novo |
Locus | Case | GU defects | Associated anomalies | Concurrent G-banded karyotype | Array platform | CNV(Signifi-cance) | Rearrangements seen in CMA | Min. size (Mb) | Secondary FISH | Min. genes | Inheritance |
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#2 | Hypospadias, Cryptorchidism | None | 46, XY | CMA (Oligo V6.5) | Loss (P) | arr cgh 2q22.2q22.3(RP11-734C21->RP11-294G19)x1 | 2 | ish del(2)(q22.3q22.3)(RP11-249G19-) | 9 | Unavailable |
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#5 | Hypospadias (midshaft) | None | 46, XY | CMA (Oligo V6.3) | Gain (P) | arr cgh 5p15.31(RP11-46O23)x3 | 0.065 | n/a, * | 1 | Present in maternal DNA |
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#17 | Hypospadias | None | n/a | CMA (Oligo V6.2) | Loss (P) | arr cgh 12p13.31p13.2(RP11-69M1->RP11-656E20)x1 | 2.3 | ish del(12)(p13.31p13.31)(RP11-69M1-)dn | 65 | De Novo |
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#20 | Hypospadias | Cleft palate | 46,XY | CMA (Oligo V6.5) | Loss (P) | arr cgh 16p11.2(29729970 - 29861142)x1 | 0.131 | ish del(16)(p11.2p11.2)(RP11-301D18-)dn | 10 | De Novo |
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#34 | Hypospadias (penoscrotal) | None | 46, XY | CMA (Oligo V6.3) | Gain (P) | arr cgh Xq28 (RP11-479B17)x3 | 0.159 | n/a, * | 1 | Unavailable |
Locus | Case | GU defects | Associated anomalies | Concurrent G-banded karyotype | Array platform | CNV (Signifi-cance) | Rearrangements seen in CMA | Min. size (Mb) | Secondary FISH | Min. genes | Inheritance |
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#3 | Hypospadias (Glanular) | None | 46, XY | CMA (Oligo V6.3) | Gain (UCS) | arr cgh 4q35.2(RP11-354H17)x3 | 0.075 | n/a, * | 0 | Present in maternal DNA |
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#7 | Cryptorchidism (inguinal) | None | 46, XY | CMA (Oligo V6.3) | Gain (UCS) | arr cgh 5p15.2(RP11-327L20)x3 | 0.1 | n/a, * | 1-8 | Present in maternal |
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#8 | Ambiguous Genitalia (Referral) | Mild Developmental Delay, Mental Retardation, Failure To Thrive | n/a | CMA (Oligo V6.3) | Loss (UCS) | arr cgh 7p22.1(RP11-160E17)x1 | 0.16 | ish del(7)(p22.1p22.1)(RP11-160E17dim) | 5 | Present in maternal DNA |
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#9 | Swyer Syndrome | None | 46,XY,del(9)(p23) | CMA (V.5.0) | Gain (UCS) | arr cgh 7p22.3(RP11-90P13->RP1-164D18 16D1S)X3, 9p24.3 (RP11-165F24->RP11-31F19)X1 | 0.25 | n/a, * | 3 | Unavailable |
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#11 | Hypospadias | Developmental Delay, mental retardation | 46,XY | CMA (V.6.1) | Gain (UCS) | arr cgh 8p23.2(RP11-82K8)x3 | 0.05 Kb | nuc ish dup(8)(p23.2)(RP11-82K8x3) | 1 | Unavailable |
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#10 | Ambiguous Genitalia (Referral) | None | 46, XY | CMA (V.5.0) | Loss (UCS) | arr cgh 8q12.2(RP11-414L17->RP11-174G1)x1 | 0.41 | ish del(8)(q12.2q12.2)(RP11-33I11-) | 4 | Unavailable |
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#6 | Ambiguous Genitalia (Referral) | None | 46,XY,der(5)(qter->q34::p14->qter) | CMA (Oligo V6.2) | Loss (UCS) | arr cgh 16p13(RP11-349E19)x1, 5p15.33p14.2(RP11-487N22->RP11-91L13)x1 | 0.14 | nuc ish dup(16)(q24.3) (RP11-566K11x3) | 1 | Unavailable |
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#21 | Hypospadias (corona) | None | 46,XY | CMA (Oligo V6.3) | Gain (UCS) | arr cgh 16q24.3 (RP11-566K11)x3 | 0.078 | nuc ish dup(16)(q24.3) (RP11-566K11x3) | 9 | Not in maternal. Paternal unavailable |
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#32 | Cryptorchidism (inguinal) | Spina Bifida | 46, XY | CMA (Oligo V6.3) | Gain (UCS) | arr cgh Xq12(RP11-349K4)x3 | 0.07 | n/a, * | 0 | Present in maternal DNA |
Regardless of the GU condition, the size of CMA detected anomalies ranged from 50 kilobases to 57.4 Mb with an average defect size of 5.5 Mb, which is at the limit of the resolution of routine karyotype (
Interestingly, in three unrelated CMA screened patients (27, 28 and 30;
The inheritance of the FISH-confirmed CMA defects was investigated by CMA testing. Parental samples were not available for all patients, leading to an underestimation of the clinically significant abnormalities in the present evaluation.
ID | Locus | DSD diagnosis | CNV | Start Position | Size (Mb) | Genes | % In Non-GU | % In GU | Karyotype | Inh | |
17 | 12p13.31p13.2 | Hypospadias | Loss | 7,987,984 | 2.306 | 65 | 0.01 | 1.11 | 1.9×10−2 | 46,XY |
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20 | 16p11.2 | Hypospadias | Loss | 29,729,970 | 0.131 | 10 | 0.07 | 1.11 | 5.7×10−2 | 46,XY |
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34 | Xq28 | Hypospadias | Gain | 154,703,321 | 0.158 | 1 | 0 | 2.22 | 9.9×10−3 | 46,XY |
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33 | Xq28 | Cryptorchidism | Gain | 154,703,321 | 0.158 | 1 | 0 | 2.22 | 9.9×10−3 | 46,XY |
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16 | 10p14 | Cryptorchidism | Gain | 12,011,806 | 0.064 | 3 | 0.02 | 1.11 | 2.9×10−2 | n/a |
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1 | 1p36.33 | Ambiguous Genitalia | Loss | 799,476 | 1.257 | 65 | 0.17 | 1.11 | 1.4×10−1 | 46,XX |
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12 | 9p23p24.3 | Ambiguous Genitalia (Gonadal dysgenesis) | Loss | 356,238 | 9.774 | 66 | 0.04 | 2.22 | 1.4×10−3 | 46,XY,der(9)del(9)(p23)dup(9)(p23p12) |
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13 | 9p24.1-pter | Ambiguous Genitalia (Gonadal dysgenesis) | Loss | 1 | 6.785 | 58 | 0.04 | 2.22 | 1.4×10−3 | 46,XY,der(9)del(9)(p24pter)dup(9)(p23p12) |
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9 | 9p24.3 | Ambiguous Genitalia (Gonadal Dysgenesis) | Loss | 356,238 | 0.259 | 4 | 0.04 | 2.22 | 1.4×10−3 | 46,XY,del(9)(p23) |
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22 | 19q12q13.11 | Ambiguous Genitalia | Loss | 33,828,527 | 5.638 | 49 | 0 | 1.11 | 9.9×10−3 | 46,XY |
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Minimal size of the spontaneous aberrations (Mb) and the number of the encompassing HGNC (Hugo Gene Nomenclature Committee) genes (G) (NCBI Build v35.1) were indicated.
Abbreviations: Inh: Inheritance,
Sample Group | Ratio | |||
Genitourinary Defects | 90 | 10 | 0.11 | 6.08×10−12 |
Non-Genitourinary Defects | 8951 | 28 | 0.003 |
To a lesser extent, imbalances inherited from a phenotypically normal maternal parent were also considered since the rearrangements may be causative without necessarily translating into similar abnormal GU traits in the female genitourinary tract. Thus, maternally inherited copy changes were considered as of unclear clinical significance and noted as: (i) deletion in 7p22.1 for ambiguous genitalia; (ii) duplications in 4q35.2 and 5p15.31 for hypospadias; (iii) duplication in 5p15.2 and in the androgen receptor insensitivity region, Xq12 for cryptorchidism (
Hence, the present analysis shed light on spontaneous chromosomal rearrangements affecting novel and unsuspected gene-enriched regions that have potential to contribute to the pathogenesis of human genital development.
The causal link of the CMA defects to the GU phenotype was further strengthened by the fact that common overlapped loci were shared by unrelated probands having similar genital defects. Spontaneous deletion of the 9p23p24 region was found in patients 9, 12, and 13, all with gonadal dysgenesis (
In addition to the 9p region, the locus Yp11.31 was an expected recurrent hit in patients with ambiguous genitalia, since it encompasses
Identical unique loci were affected in patients presenting distinct genital phenotypic traits, which suggest that structural perturbations within these segments may alter master regulator(s) of multiple processes of human sexual development. Indeed, a large deletion of the subtelomeric cytoband 5p15 detected in the patient 6 with genital ambiguity overlapped a region duplicated in patient 5 with hypospadias (
The DiGeorge syndrome critical region 22q11.2 was also found duplicated in patients with ambiguous genitalia, while its deletion was seen in patients presenting with GU abnormalities in association with Smith-Lemli-Opitz syndrome or Wilms tumor (
In parallel, alterations occurring on 2q22 and Xq28 loci were found in patients with cryptochidism and hypospadias (
Taken together, our findings highlight for the first time the presence of previously unrecognized chromosomal imbalances as potential genetic risks factors in disorders of sexual development and illustrate how a microarray-based technology provides a powerful alternative to traditional cytogenetic and gene-mapping approaches for discovering contributing factors in disease of complex etiology.
The development of male reproductive system is a complex process controlled by delicate networks that specify sex-specific differentiation, organogenesis and endocrine function. The fragility of these regulatory cascades is illustrated by the high prevalence of genitourinary defects in newborns. These inborn urogenital anomalies present difficult challenges for the parents and the physicians, as care of these children is complicated by surgical, psychological, social and sexual concerns. The gold standard for genetic diagnosis remains a karyotype analysis and an endocrine profile but findings in intersex cases are not always informative. Indeed, only a small portion of these developmental aberrations can be attributed to defects in the synthesis of testosterone or adrenal steroid hormones, receptor alterations, exogenous modifiers or obvious numerical and structural chromosomal alterations, such as Klinefelter syndrome. The underlying causes of the majority of “idiopathic” cases remain to be discovered. In this study, the use of a clinically validated microarray (CMA) revealed the existence of cryptic imbalances strongly associated with defects of urogenital development or recurrently found in patients with DSD. These chromosomal aberrations were mostly too small to be detected by the routinely ordered karyotype, which has a limited resolution of 5–10 Mb, depending on the quality of chromosome preparations. Many of these genomic anomalies went also largely undetected because they were located in subtelomeric loci, which are notoriously difficult to characterize by G-banding. Moreover, mild or isolated cases of hypospadias and cryptorchid patients are usually not referred for genetic testing, while this study proved that this subset of patients harbored structural variation that may convey defective urogenital traits.
Most of the detected chromosomal aberrations encompassed one to a few hundred genes including known gonad-determining genes (
Our findings provide support for the genomic basis of human disorders of sexual development and call for genome-wide CNV screenings which may, due to their extended coverage, reveal a higher proportion of germline mutations associated with urogenital defects. Enrichment in candidate genes for human sexual development is subsequently bound to increase. Our present study using the clinically established CMA platform was motivated by a rapid translation of our findings to the clinical arena. Molecular testing, such as with CMA, could significantly impact patient care by assisting the pediatric urologists and neonatologists in diagnosis. Genetic counseling offered to families based on the identification of pathogenic rearrangements may provide parents with essential clinical information pertaining to the child's diagnosis and permit proper estimates of the risk of recurrence for subsequent pregnancies.
In conclusion, this study presented structural DNA variation as a potential underlying etiology for human disorders of sexual development. Frequent disease-causing submicroscopic gains and losses of DNA segments were detected across the genome and strongly associated with defective urogenital traits. This has been achieved with significantly higher resolution and greater clinical yield than standard routine karyotype, thus making this array-based CGH screen as a genetic test of choice in diagnosis. While GU defects cases arise among newborns without clear etiology, this study offers novel loci to dissect for determining key genes involved in the human sexual development.
We would like to thank all the referring physicians and especially Drs. Edmond T. Gonzales, Lars Cisek, David R. Roth and Eric Jones, the affected individuals and their family members who participated in this study. We thank Dr. Kenneth McElreavy (Pasteur Institute, Paris, France) who provided two patient samples with gonadal dysgenesis for this study. We thank Drs. John Belmont, Lisa White and Hao Liu for their cooperation. We also thank Matthew Folsom for his excellent technical assistance.