A fetus with 19q13.11 microdeletion presenting with intrauterine growth restriction and multiple cystic kidney

Shin-Yu Lin, Chien-Nan Lee 3 , Tai-Chang Chen 2 , Mei-Ping Tu 3 , Chiou-Ya Lin 3 , Tung-Yao Chang 4 ,  and Yi-Ning Su
  • 1 Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
  • 2 Department of Obstetrics and Gynecology, National Taiwan University Hospital, Hsin Chu branch, Hsin Chu, Taiwan
  • 3 Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
  • 4 Taiji Fetal Medical Center, Taipei, Taiwan
  • 5 Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
  • 6 Graduate Institute of Clinical Genomics, National Taiwan University, No. 7 Chung-Shan South Road, Taipei, Taiwan
Shin-Yu Lin, Chien-Nan Lee, Tai-Chang Chen, Mei-Ping Tu, Chiou-Ya Lin, Tung-Yao Chang and Yi-Ning Su

Abstract

Background: Constitutional deletions of chromosome 19q were rarely reported in the literature. The array-comparative genome hybridization (CGH) helps to identify four children with 19q13 microdeletion and the microdeletion of 19q13.11 is a recent emerging syndrome. We report one fetus with 19q12q13.12 deletion diagnosed prenatally and compare with five cases in the literature.

Case: The 29 year-old woman was at the 27th week of gestation. Prenatal ultrasound revealed severe intrauterine growth restriction and left side multiple cystic kidney with normal amniotic fluid index. Cordocentesis was performed for karyotyping and array CGH.

Results: The karyotype of the fetus was considered as normal male. The BAC array CGH identified one deletion at chromosome 19q12q13.12. The oligonucleotide array CGH further characterized the size of the breakpoint (chr19:35,116, 199-42,994,905). After counselling, the pregnancy was terminated at the 28th week of gestation. The aborted fetus had hypospadias and facial dysmorphisms.

Conclusions: Although a complete genotype-phenotype may not be established in these patients with 19q13 deletions, they shared some unique phenotypes and facial dysmorphisms. The clinician should keep in mind when anomalies are detected prenatally, array CGH may help to identify the etiology, which is critical for counselling.

Introduction

Fewer than ten cases with constitutional deletions of chromosome 19 have been reported in the literature. Such a paucity of patients is likely related to the absence of a distinct banding pattern on this chromosome [10]. Using advanced molecular cytogenetic technology, the array-comparative genome hybridization (CGH) helped to identify four children with 19q13 microdeletion in 2009 [10, 13]. Although there was some phenotypic variability, these patients shared some common findings and the microdeletion of 19q13.11 was a recent emerging syndrome. The ever reported five cases with overlapped 19q13.11 deletion had phenotypes including intrauterine and postnatal growth retardation, microcephaly, feeding problems, ectodermal dysplasia, cutis aplasia over the posterior occiput, hypospadias, and clinodactyly of the fourth finger. We report detailed studies of one fetus with 19q12q13.12 deletion diagnosed prenatally and compare the findings with five previously reported cases in the literature [9, 10, 13].

Clinical report and methods

The 29-year-old mother, gravida 2, para 1, was Asian. Her first baby was a healthy girl. Prenatal ultrasound examination was performed at the 27th week of gestation because the fetus was small for gestational age. The biparietal distance of the fetus was 55 mm (50th percentile for 23 weeks), head circumference 210 mm (50th percentile for 23 weeks), and femur length 45 mm (50th percentile for 25 weeks). The fetal measurements corresponded to 23 weeks of gestation with mild increased resistance of the umbilical artery (S/D ratio, 3.6; 71st percentile; pulse index, 1.52; normal waveform). Pulse index of right and left uterine arteries were 0.53 and 1.28, respectively, and no notch was noted. The ultrasound study also showed a multicystic left kidney and a normal-sized right kidney, normal amniotic fluid index (13.5 cm), and female genitalia. A fetal echocardiogram and color flow Doppler ultrasound studies showed no abnormalities. Fetal breathing movement, fetal movement, and fetal tone were normal.

Cytogenetic studies

Cordocentesis was performed at the 27th week of gestation. Standard karyotyping using G-banding analysis was performed on the lymphocytes in the cord blood and the peripheral blood of the parents.

Array CGH studies

Genomic DNA was extracted from the fetal cord blood and the parent’s peripheral blood using the QIAamp DNA Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. DNA concentration was determined with NanoDrop ND 1000 spectrophotometer and software (NanoDrop Technologies, Berlin, Germany). Bacterial artificial clones (BAC) based array CGH was performed using the BAC HD Scan™ v2 microarray (CMDX, Irvine, CA, USA) with a resolution of 1 Mb according to the manufacturer’s instructions. Oligonucleotide array CGH, Oligo HD Scan™ v.1 (CMDX, Irvine, CA, USA), with 105,000 oligo probes spaced at approximately 10- to 35-kb intervals across the genome, was used to further characterize the extend of the deletion.

Multiplex PCR

Multiplex PCR assays were performed to identify the genetic dosage of six genes near the breakpoint (Figure 1). The sequences of primers were listed in Supplementary Table 1. The multiplex PCR was performed in a total volume of 25 µL containing 100 ng of genomic DNA, 0.04 – 0.4 µM of each primer, 200 µM dNTPs, 0.1 units of AmpliTaq GoldTM enzyme (PE Applied Biosystems), and 2.5 µL of GeneAmp 10× buffer II (10 mM Tris-HCl, pH 8.3, 50 mM KCl), in 2 mM MgCl2 as provided by the manufacturer.

The multiplex PCR products were analyzed by the high-performance DNA analysis capillary electrophoresis system with the GCK-500 cartridge kit (eGene, Irvine, CA, USA). The quantification of DNA fragments was based on the integrated peak area. The target gene copy numbers were calculated by adjusting the relative known dosage of the KRIT1 gene. We used the following equation to calculate the copy number of the target gene in the case (C) as compared with the mean of the wild type (W):

article image

Figure 1
Figure 1

Multiplex PCR revealed one allelic deletion in the C19orf2 gene, SCGBL gene, USEF2 gene, and ZFP30 genes but not in the CCNE1 gene or the SIPA1L3 gene.

#FGFR2 gene; *KRIT gene.

Citation: Case Reports in Perinatal Medicine 1, 1-2; 10.1515/crpm-2012-0001

Results

The karyotype of the fetus was considered as normal male by standard G-banding method (Figure 2A). With the BAC array CGH, nevertheless, we identified one 5.84-Mb deletion at the long arm of chromosome 19 in the fetus. A total of 13 BACs (from RP11-13D7 to RP11-587I9) spanning a region from 35.45 to 41.29 Mb in 19q12q13.12 had a significantly low test/reference log2 intensity ratio (Figure 2B). The oligonucleotide array CGH further characterized the size of the deletion and the breakpoint (chr19:35,116,199–42,994,905) (Figure 2C). Multiplex PCR revealed one allelic deletion in the C19orf2 gene, SCGBL gene, USEF2 gene, and ZFP30 genes but not in the CCNE1 gene or the SIPA1L3 gene in this case (Figure 1). The BAC array CGH analyses of the parental samples demonstrated that the deletion occurred de novo.

Figure 2
Figure 2

(A) G-banding of chromosome 19. (B) BAC array CGH revealed the deletion from 19q12 to 19q13.12. (C) Oligonucleotide array CGH revealed the deletion of chromosome 19 from 35,116,199 to 42,994,905 bp.

Citation: Case Reports in Perinatal Medicine 1, 1-2; 10.1515/crpm-2012-0001

After genetic counseling, the pregnancy was terminated at the 28th week of gestation. A fetocide was performed with 6 mL potassium chloride at the fetal heart under sonographic guidance. Misoprostol 50 µg was then administered intravaginally once and then thrice orally every 6 h. The abortus was expulsed with intact amniotic bag 26 h later. The aborted fetus weighted 402 g and had ambiguous genitalia and facial dysmorphism including long face, high forehead, retrognathia, thin lips, maxillary protrusion, broad nasal root, and large posteriorly angulated and low-set ears (Figure 3). The couple refused an autopsy of the abortus.

Figure 3
Figure 3

The aborted fetus had ambiguous genitalia and facial dysmorphism including long face, high forehead, retrognathia, thin lips, maxillary protrusion, broad nasal root, and large posteriorly angulated and low-set ears.

Citation: Case Reports in Perinatal Medicine 1, 1-2; 10.1515/crpm-2012-0001

Discussion

We described the six patients with an interstitial deletion overlapping the 19q13.11 region. The 5.84-Mb microdeletion was initially detected by BAC base array CGH with 1-Mb resolution. The breakpoint was extended to 7.88 Mb by the oligonucleotide array with 35-kb resolution. In addition, most array CGH results were validated by fluorescence in situ hybridization (FISH) technology [4, 12, 14]. We designed the multiplex PCR assays to further confirm the breakpoints. The advantage of the method is fluorescence-independent, self-designed, and less expensive. In terms of length of time, the FISH method requires 2–3 days, which involves cell culture, whereas multiplex PCR requires 3 h [8].

Because this pregnancy was terminated, we were not able to evaluate the developmental characteristics, motor functions, or the cutis aplasia in the midline of the scalp. The abortus, nevertheless, shared some overlapping phenotypes with the other five cases reported in the literature. First, all of the cases with 19q13.11 microdeletion had intrauterine growth retardation (IUGR). Second, all the male patients had hypospadias. Third, these patients had typical facial dysmorphisms, such as thin lips (6/6), micro/retrognathia (6/6), large ears (4/6), and long face (4/6). In the deleted region of our case, there were over 40 zinc finger protein genes. Whether the haploinsufficiency of these zinc finger cluster in the long arm of chromosome 19 might contribute to the phenotypes needs to be further investigated. Schuurs-Hoeijmakers et al. [13] had refined the critical region to 750 kb and identified two candidate genes, LSM14A and UBA2 gene, that might be responsible for the 19q13.11 microdeletion syndrome [13].

Of the six cases with 19q deletion, only our patient and the patient of Kulharya et al. [9] had multicystic kidneys. However, the overlapping deleted regions (1 Mb) between these two cases contain mainly zinc finger protein genes and some cDNA with unknown molecular function (Figure 4). Furthermore, within the 7.8-Mb deleted region of our patient, there are several genes that may be associated with abnormal renal function. The interrupted USF2 gene has been reported in a case with a de novo translocation, t(6;19)(p21;q13.1), and multicystic renal dysplasia [6]. The UPK1A gene encodes uroplakin protein, which may play a role in normal bladder epithelial physiology [7]. The NPHS1 gene is primarily expressed in the renal tissue, and the mutations in this gene result in congenital nephrosis, characterized by severe proteinuria and loss of the slit diaphragm and foot processes [1, 5]. Although a complete genotype-phenotype correlation cannot be established by these six patients, the 19q13.11 microdeletion syndrome may have some recognizable facial dysmorphism and share some phenotypes.

Figure 4
Figure 4

Six cases with 19q13.2 deletions in the literature.

Citation: Case Reports in Perinatal Medicine 1, 1-2; 10.1515/crpm-2012-0001

The patient of Kulharya et al. [9] had the largest deleted region (about 11 Mb) and was identified initially by karyotyping. The other four cases reported by Malan et al. [10] and Schuurs-Hoeijmakers et al. [13] were diagnosed postnatally by array CGH technologies due to the small deleted size and the limited resolution of standard karyotyping. In our patient, standard G-banding also failed to identify the etiology of the abnormal sonographic findings. According to the literature [3], unilateral multicystic dysplastic kidney disease with normal karyotype and adequate amniotic fluid is a reassuring finding. However, this reported case also had IUGR, which prompted us to do further workup. By applying the array CGH, we detected the microdeletion at chromosome 19q12q13.12, which involved not only the 19q13.11 but also the SCN1B gene and the COX6B1 gene; the mutations in the former gene may result in generalized epilepsy with febrile seizures and arrhythmia, whereas the mutation in the latter gene are reported in patients with severe infantile encephalomyopathy [2, 11, 15, 16]. Under the situation, the information was critical for the parents to make decisions at prenatal counseling. The case demonstrated the benefit of array CGH in the prenatal application.

Conclusions

Array CGH helps to identify microdeletions and provides higher resolution than G-banding karyotype. The cases with microdeletion of 19q13.11 share several common phenotypes and microdeletion of 19q13.11 is a recent emerging syndrome.

The authors thank the family who participated in the test and shared the pictures of the abortus. We also acknowledge Dr. Mercedes E. Gorre and Jaeweon Kim from Combimatrix Molecular Diagnostics (Irvine, CA, USA) to their support in the analysis of BAC and oligonucleotide array CGH.

a

This work was supported by a grant from the National Science Council (grant NSC98-2314-B-002-142).

The authors stated that there are no conflicts of interest regarding the publication of this article.

References

  • [1]

    Aya K, Shimizu J, Ohtomo Y, Satomura K, Suzuki H, Yan K, et al. NPHS1 gene mutation in Japanese patients with congenital nephrotic syndrome. Nephrol Dial Transplant. 2009;24:2411–4.

  • [2]

    Brodie MJ. Epilepsy: randomised trials and genetic tribulations. Lancet Neurol. 2008;7:7–8.

  • [3]

    Estroff JA, Mandell J, Benacerraf BR. Increased renal parenchymal echogenicity in the fetus: importance and clinical outcome. Radiology. 1991;181:135–9.

  • [4]

    Fernandez L, Nevado J, Santos F, Heine-Suner D, Martinez-Glez V, Garcia-Minaur S, et al. A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review. BMC Med Genet. 2009;10:48.

  • [5]

    Gigante M, Monno F, Roberto R, Laforgia N, Assael MB, Livolti S, et al. Congenital nephrotic syndrome of the Finnish type in Italy: a molecular approach. J Nephrol. 2002;15:696–702.

  • [6]

    Groenen PM, Garcia E, Thoelen R, Aly M, Schoenmakers EF, Devriendt K, et al. Isolation of cosmids corresponding to the chromosome breakpoints of a de novo autosomal translocation, t(6;19)(p21;q13.1), in a patient with multicystic renal dysplasia. Cytogenet Cell Genet. 1996;75: 210–5.

  • [7]

    Hall GD, Weeks RJ, Olsburgh J, Southgate J, Knowles MA, Selby PJ, et al. Transcriptional control of the human urothelial-specific gene, uroplakin Ia. Biochim Biophys Acta. 2005;1729:126–34.

  • [8]

    Hung CC, Lin SY, Lin SP, Niu DM, Lee NC, Cheng WF, et al. Identification of CpG methylation of the SNRPN gene by methylation-specific multiplex PCR. Electrophoresis. 2009;30:410–6.

  • [9]

    Kulharya AS, Michaelis RC, Norris KS, Taylor HA, Garcia- Heras J. Constitutional del(19)(q12q13.1) in a three-year-old girl with severe phenotypic abnormalities affecting multiple organ systems. Am J Med Genet. 1998;77:391–4.

  • [10]

    Malan V, Raoul O, Firth HV, Royer G, Turleau C, Bernheim A, et al. 19q13.11 deletion syndrome: a novel clinically recognisable genetic condition identified by array comparative genomic hybridisation. J Med Genet. 2009;46:635–40.

  • [11]

    Massa V, Fernandez-Vizarra E, Alshahwan S, Bakhsh E, Goffrini P, Ferrero I, et al. Severe infantile encephalomyopathy caused by a mutation in COX6B1, a nucleus-encoded subunit of cytochrome c oxidase. Am J Hum Genet. 2008;82:1281–9.

  • [12]

    Maurin ML, Labrune P, Brisset S, Le Lorc’h M, Pineau D, Castel C, et al. Molecular cytogenetic characterization of a 4p15.1-pter duplication and a 4q35.1-qter deletion in a recombinant of chromosome 4 pericentric inversion. Am J Med Genet A. 2009;149A:226–31.

  • [13]

    Schuurs-Hoeijmakers JH, Vermeer S, van Bon BW, Pfundt R, Marcelis C, de Brouwer AP, et al. Refining the critical region of the novel 19q13.11 microdeletion syndrome to 750 Kb. J Med Genet. 2009;46:421–3.

  • [14]

    Shaffer LG, Bui TH. Molecular cytogenetic and rapid aneuploidy detection methods in prenatal diagnosis. Am J Med Genet C Semin Med Genet. 2007;145C:87–98.

  • [15]

    Wallace RH, Scheffer IE, Parasivam G, Barnett S, Wallace GB, Sutherland GR, et al. Generalized epilepsy with febrile seizures plus: mutation of the sodium channel subunit SCN1B. Neurology. 2002;58:1426–9.

  • [16]

    Watanabe H, Darbar D, Kaiser DW, Jiramongkolchai K, Chopra S, Donahue BS, et al. Mutations in sodium channel beta1- and beta2-subunits associated with atrial fibrillation. Circ Arrhythm Electrophysiol. 2009;2:268–75.

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  • [1]

    Aya K, Shimizu J, Ohtomo Y, Satomura K, Suzuki H, Yan K, et al. NPHS1 gene mutation in Japanese patients with congenital nephrotic syndrome. Nephrol Dial Transplant. 2009;24:2411–4.

  • [2]

    Brodie MJ. Epilepsy: randomised trials and genetic tribulations. Lancet Neurol. 2008;7:7–8.

  • [3]

    Estroff JA, Mandell J, Benacerraf BR. Increased renal parenchymal echogenicity in the fetus: importance and clinical outcome. Radiology. 1991;181:135–9.

  • [4]

    Fernandez L, Nevado J, Santos F, Heine-Suner D, Martinez-Glez V, Garcia-Minaur S, et al. A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review. BMC Med Genet. 2009;10:48.

  • [5]

    Gigante M, Monno F, Roberto R, Laforgia N, Assael MB, Livolti S, et al. Congenital nephrotic syndrome of the Finnish type in Italy: a molecular approach. J Nephrol. 2002;15:696–702.

  • [6]

    Groenen PM, Garcia E, Thoelen R, Aly M, Schoenmakers EF, Devriendt K, et al. Isolation of cosmids corresponding to the chromosome breakpoints of a de novo autosomal translocation, t(6;19)(p21;q13.1), in a patient with multicystic renal dysplasia. Cytogenet Cell Genet. 1996;75: 210–5.

  • [7]

    Hall GD, Weeks RJ, Olsburgh J, Southgate J, Knowles MA, Selby PJ, et al. Transcriptional control of the human urothelial-specific gene, uroplakin Ia. Biochim Biophys Acta. 2005;1729:126–34.

  • [8]

    Hung CC, Lin SY, Lin SP, Niu DM, Lee NC, Cheng WF, et al. Identification of CpG methylation of the SNRPN gene by methylation-specific multiplex PCR. Electrophoresis. 2009;30:410–6.

  • [9]

    Kulharya AS, Michaelis RC, Norris KS, Taylor HA, Garcia- Heras J. Constitutional del(19)(q12q13.1) in a three-year-old girl with severe phenotypic abnormalities affecting multiple organ systems. Am J Med Genet. 1998;77:391–4.

  • [10]

    Malan V, Raoul O, Firth HV, Royer G, Turleau C, Bernheim A, et al. 19q13.11 deletion syndrome: a novel clinically recognisable genetic condition identified by array comparative genomic hybridisation. J Med Genet. 2009;46:635–40.

  • [11]

    Massa V, Fernandez-Vizarra E, Alshahwan S, Bakhsh E, Goffrini P, Ferrero I, et al. Severe infantile encephalomyopathy caused by a mutation in COX6B1, a nucleus-encoded subunit of cytochrome c oxidase. Am J Hum Genet. 2008;82:1281–9.

  • [12]

    Maurin ML, Labrune P, Brisset S, Le Lorc’h M, Pineau D, Castel C, et al. Molecular cytogenetic characterization of a 4p15.1-pter duplication and a 4q35.1-qter deletion in a recombinant of chromosome 4 pericentric inversion. Am J Med Genet A. 2009;149A:226–31.

  • [13]

    Schuurs-Hoeijmakers JH, Vermeer S, van Bon BW, Pfundt R, Marcelis C, de Brouwer AP, et al. Refining the critical region of the novel 19q13.11 microdeletion syndrome to 750 Kb. J Med Genet. 2009;46:421–3.

  • [14]

    Shaffer LG, Bui TH. Molecular cytogenetic and rapid aneuploidy detection methods in prenatal diagnosis. Am J Med Genet C Semin Med Genet. 2007;145C:87–98.

  • [15]

    Wallace RH, Scheffer IE, Parasivam G, Barnett S, Wallace GB, Sutherland GR, et al. Generalized epilepsy with febrile seizures plus: mutation of the sodium channel subunit SCN1B. Neurology. 2002;58:1426–9.

  • [16]

    Watanabe H, Darbar D, Kaiser DW, Jiramongkolchai K, Chopra S, Donahue BS, et al. Mutations in sodium channel beta1- and beta2-subunits associated with atrial fibrillation. Circ Arrhythm Electrophysiol. 2009;2:268–75.

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Continuous readers’ interest and significant relevance of case reports inspired the Editors and Publishers of the Journal of Perinatal Medicine (JPM) to found the journal Case Reports in Perinatal Medicine. (CRPM) The aims & scope of CRPM are very similar to those of JPM: both journals publish interdisciplinary, innovative, evidenced-based and basic science research that is informative and useful for daily clinical practice.

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  • View in gallery

    Multiplex PCR revealed one allelic deletion in the C19orf2 gene, SCGBL gene, USEF2 gene, and ZFP30 genes but not in the CCNE1 gene or the SIPA1L3 gene.

    #FGFR2 gene; *KRIT gene.

  • View in gallery

    (A) G-banding of chromosome 19. (B) BAC array CGH revealed the deletion from 19q12 to 19q13.12. (C) Oligonucleotide array CGH revealed the deletion of chromosome 19 from 35,116,199 to 42,994,905 bp.

  • View in gallery

    The aborted fetus had ambiguous genitalia and facial dysmorphism including long face, high forehead, retrognathia, thin lips, maxillary protrusion, broad nasal root, and large posteriorly angulated and low-set ears.

  • View in gallery

    Six cases with 19q13.2 deletions in the literature.