Prenatal diagnosis and molecular cytogenetic characterization of a de novo
interstitial deletion of 7q (7q22.1
q31.1)
Chih-Ping Chen a,b,c,d,e,f,g *, Shing-Jyh Chang h,i, Schu-Rern Chern b, Peih-Shan Wu j,Yu-Ting Chen b, Jun-Wei Su a,k, Wen-Lin Chen a and Wayseen Wang b,l
a Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
b Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
c Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
d Department of Biotechnology, Asia University, Taichung, Taiwan
e School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
f Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan
g Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei,
Taiwan
h Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan
i Department of Molecular Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
j Gene Biodesign Co. Ltd, Taipei, Taiwan
k Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung, Taiwan
l Department of Bioengineering, Tatung University, Taipei, Taiwan
* Correspondence to: Chih-Ping Chen, MD
Department of Obstetrics and Gynecology, Mackay Memorial Hospital 92, Section 2, Chung-Shan North Road, Taipei, Taiwan
Tel: +886-2-25433535; Fax: +886-2-25433642, +886-2-25232448 E-mail: [email protected]
Highlights
We present de novo del(7)(q22.1q31.1)in a fetus.
The prenatal findings include abnormal maternal serum screening, facial cleft and hypogenitalism.
We discuss the genotype-phenotype correlation.
Abstract
We present prenatal diagnosis and molecular cytogenetic characterization of de novo interstitial deletion of 7q (7q22.1q31.1) by aCGH, FISH and QF-PCR in a fetus with an abnormal maternal serum screening result and ultrasound findings of facial cleft and hypogenitalism. We discuss the genotype-phenotype correlation and the consequence of haploinsufficiency of ZKSCAN5,
ARPC1A, CYP3A43, RELN, LAMB1, IMMP2L and DOCK4 in this case.
Keywords: 7q22-q31 deletion; chromosome 7q; facial cleft; hypogenitalism; interstitial deletion; prenatal diagnosis
Abbreviations
AVSD: atrioventricular septal defect; del: deletion; BAC: bacterial artificial chromosome; aCGH: array comparative genomic hybridization; FISH: fluorescence in situ hybridization; QF-PCR: quantitative fluorescent polymerase chain reaction; MoM: multiples of the median; AFP: -fetoprotein; uE3: unconjugated estriol; -hCG: -human chorionic gonadotrophin; PAPP-A: pregnancy-associated plasma protein A; OMIM: Online Mendelian Inheritance in Man; SNP: single nucleotide polymorphism
Chromosome 7q22-q31 deletions are rare, and most reported cases have been presented before the availability of high-resolution assays and have not been studied in detail. Schinzel (2001) concluded that the clinical patterns of del(7)(q22q31) include short stature, low-set and dysplastic ears, strabismus, epicanthic folds, macrostomia with a thin upper lip, and down-turned corners of the mouth, short neck and camptodactyly. Other abnormalities associated with del(7) (q22q31) include spina bifida occulta, blepharophimosis, glaucoma, AVSD, helical pits, preauricular tags, hypospadias, congenital contractures, seizures, mental retardation and cleft palate (Abuelo and Padre-Mendoza, 1982; Cheong et al., 2008; Dennis et al., 1977; Franceschini et al., 1978; Hull et al., 1979; Serup, 1980; Young et al., 1984).
Here, we report prenatal diagnosis and molecular cytogenetic analyses of a de novo interstitial deletion of 7q (7q22.1q31.1) by aCGH, FISH and QF-PCR in a fetus with an abnormal maternal serum screening result and abnormal ultrasound findings of facial cleft and hypogenitalism. To our knowledge, such a case has not been previously described.
2. Methods and detection
2.1. Conventional cytogenetic analysis
Routine cytogenetic analysis by G-banding techniques at the 550 bands of resolution was performed. 20 mL amniotic fluid was collected, and the sample was subjected to in situ amniocyte culture according to the standard cytogenetic protocol. Parental bloods were collected, and the samples were subjected to lymphocyte culture according to the standard blood cytogenetic protocol.
2.2. Array-CGH
Whole-genome aCGH on uncultured amniocytes derived from 10 mL amniotic fluid was performed using NimbleGen ISCA Plus Cytogenetic Array (Roche NimbleGen, Madison, WI, USA). The NimbleGen ISCA Plus Cytogenetic Array has 630,000 probes and a median resolution of 15-20 kb across the entire genome according to the manufacturer’s instruction.
2.3. FISH
FISH analysis was performed on cultured amniocytes using a 7q31.1-specific BAC probe RP11-90N13 (spectrum red) and a 7q36.3-specific BAC probe RP11-93F2 (spectrum green) according to the standard FISH protocol.
2.4. QF-PCR
QF-PCR analysis was performed on uncultured amniocytes derived from 10 mL amniotic fluid and parental bloods. Polymorphic DNA markers such as D7S818 (7q22.1), D7S1799 (7q22.1) and D7S1817 (7q31.1) were used to determine the parental origin of the deletion.
2.5. Clinical description
A 29-year-old, primigravid woman underwent second-trimester maternal serum quadruplet test for Down syndrome at 16 weeks of gestation. Maternal serum screening revealed a Down syndrome risk of 1/6 calculated from maternal age, maternal AFP level of 0.74 MoM, uE3 level of 0.49 MoM, -hCG level of 6.04 MoM and inhibin A level of 3.83 MoM. The husband was aged 30 years. The woman and her husband were non-consanguineous and healthy, and there was no family history of congenital malformations. Level II ultrasound examination revealed facial cleft, ambiguous external genitalia and hypogenitalism. The amniotic fluid amount and fetal growth were normal. Internal organs were unremarkable. Amniocentesis was performed at 20 weeks of gestation. Cytogenetic analysis of the cultured amniocytes revealed an intermediate interstitial deletion of chromosome 7q. The parental karyotypes were normal. Repeated amniocentesis was performed at 22 weeks of gestation. Whole-genome aCGH analysis on uncultured amniocytes detected a 13.45-Mb deletion at chromosome 7q22.1-7q31.1. Metaphase FISH analysis of cultured amniocytes using the 7q31.1-specific probe and 7q36.3-specific probe showed a result consistent with the findings of aCGH. QF-PCR assays showed that the deleted chromosome was from maternal origin. The parents elected to terminate the pregnancy at 24 weeks of gestation, and a 616-g malformed fetus was delivered with a median cleft lip and palate, hypertelorism, broad nasal bridge, micrognathia, low-set ears, micropenis and cryptorchidism (Fig S1). The extremities and digits were normal.
3. Results
Whole-genome aCGH analysis on uncultured amniocytes detected a 13.45-Mb deletion at chromosome 7q22.1-7q31.1, or arr cgh 7q22.1q31.1 (98,423,469-111,872,943)1 (NCBI build 37) (Fig. 1). The deleted region encompasses 220 genes and 96 OMIM genes including ZKSCAN5,
ARPC1A, CYP3A43, RELN, LAMB1, IMMP2L and DOCK4. The karyotype of cultured
amniocytes was 46,XY,del(7)(q22.1q31.1)dn (Fig. 2). Metaphase FISH analysis on cultured amniocytes showed absence of the 7q31.1-specific probe signal on the abnormal chromosome 7,
the fetus on the informative markers of D7S818 (7q22.1), D7S1799 (7q22.1) and D7S1817 (7q31.1) (Fig. 4). The deleted chromosome was from maternal origin.
4. Discussion
The present case is associated with facial dysmorphisms, median cleft lip and palate, micropenis, cryptorchidism, abnormal second-trimester maternal serum screening and a 13.45-Mb deletion encompassing chromosome 7q22.1q31.1. Cheong et al. (2008) previously reported the association of del(7)(q22.1q31.1) with an increased Down syndrome risk of 1/50 calculated from a maternal serum PAPP-A level of 0.17 MoM, a free -hCG level of 1.33 MoM and a fetal NT thickness of 1.1 mm (1.25 MoM) in the first trimester in a male fetus with hypertelorism, wide nasal bridge, low-set ears and cleft palate. In that case, the deletion was based on conventional cytogenetic analysis but lacked the fine details. Hafen and Rose (2010) reported diagnosis of a fetus with del(7)(q22q31.2) and second-trimester ultrasound abnormalities of growth delay, mild ventriculomegaly, mild renal pelviectasis and anomalous venous drainage to the superior vena cava. In that case, the first-trimester low PAPP-A level and the second-trimester low AFP and uE3 levels in the maternal serum screening results were consistent with the findings reported by Cheong et al. (2008) and ours. Park et al. (2008) reported prenatal diagnosis of a fetus with del(7) (q11.23q21.2) associated with an increased Down syndrome risk of 1/82 calculated from a low maternal serum AFP level of 0.813 MoM, a low uE3 level of 0.141 MoM and an hCG level of 1.01 MoM in the second trimester. Maternal serum screening for Down syndrome may incidentally detect chromosomal abnormalities other than common aneuploidies (Chen et al., 2011, 2012, 2013). The present pregnant woman belongs to the low-risk group of aneuploidy based on maternal age. She underwent amniocentesis because of a positive screen risk of 1/6 for trisomy 21 calculated by relatively low levels of AFP and uE3, and abnormally high levels of -hCG and inhibin A. The present case shows that fetuses with del(7)(q22.1q31.1) can be associated with low levels of AFP and uE3, and high levels of -hCG and inhibin A, and a corresponding high Down syndrome risk in the second trimester maternal serum screening. We suggest that an abnormal second-trimester maternal serum quadruplet test result may be a distinctive prenatal feature in the pregnancy associated with fetal intermediate interstitial 7q deletion.
The present case was not associated with ectrodactyly. Ectrodactyly has been part of the phenotype of del(7)(q21q31) (Montgomery et al., 2000; Morey and Higgins, 1990; Yilmaz et al., 2005). The locus responsible for split-hand/foot malformation-1 (SHFM1) (OMIM 183600) and SHFM1 with sensorineural hearing loss (SHFM1D) (OMIM 220600) has been mapped to 7q21.3. SHFM1D is caused by mutations in the DLX5 gene (OMIM 600028). Ectrodactyly, ectrodermal dysplasia and cleft lip/palate syndrome 1 (EEC1) (OMIM 129900) has been linked to 7q11.2-q21.3. The present case did not have haploinsufficiency of the genes proximal to 7q22 and therefore presented no phenotype of ectrodactyly.
The present case presented facial cleft and hypogenitalism on prenatal ultrasound. Prenatal diagnosis of facial cleft should alert chromosomal abnormalities. Chromosomal abnormalities can be found in 30-50% of the fetuses with facial cleft (Bergé et al., 2001; Clementi et al., 2000; Nicolaides et al., 1993; Nyberg et al., 1995; Snijders et al., 1996). Nyberg et al. (1995) reported chromosomal abnormalities in 30.8% (20/65) of the fetuses with facial cleft. In a study of the correlation of chromosomal abnormalities with the types of facial clefts, Nyberg et al. (1995) found chromosomal abnormalities in 0% (0/5) of the cases with unilateral cleft lip, in 20% (3/15) with unilateral cleft lip and palate, in 30% (6/20) with bilateral cleft lip and palate, in 52.4% (11/21) of the fetuses with median cleft lip and palate. Bergé et al. (2001) reported chromosomal abnormalities in 51.4% (36/70) of the fetuses with facial cleft and additionally found chromosomal abnormalities in 0% (0/3) of the cases with unilateral cleft lip, in 32% (8/25) with unilateral cleft lip and palate, in 58.9% (17/29) with bilateral cleft lip and palate, and in 81.8% (9/11) with median cleft lip and palate. Hypogenitalism such as cryptorchidism has been noted in the patient with a microdeletion of 7q22.1-q22.3 (Al-Hassnan et al., 2011), and facial cleft has been observed in the patient with del(7)(q21.2q31.1) (Cheong et al., 2008). In a review of 7 patients (1 male and 6 females) with del(7)(q21q31), Young et al. (1984) found facial cleft in one patient and hypogenitalism in a male patient.
The present case had haploinsufficiency of the genes of ZKSCAN5, ARPC1A, CYP3A43, RELN,
LAMB1, IMMP2L and DOCK4. ZKSCAN5 (OMIM 611272), also known as ZFP95 or KIAA1015,
is a spermatogenesis-specific zinc finger gene. ZKSCAN5 is highly expressed in testis, epididymis, seminal vesicle and prostate (Dreyer et al., 1999; Nagase et al., 1999; Weissig et al., 2003) and has been suggested to influence neuronal function (Ward et al., 2007). Recently, SNPs
dehydroepiandrosterone sulphate (DHEAS) which is a circulating steroid secreted by adrenal glands (Zhai et al., 2011). RELN (OMIM 600514) encodes a glycoprotein reelin that arrests neuronal migration and promotes normal cortical lamination (Dulabon et al., 2000). Human
RELN mutations are associated with autosomal recessive lissencephaly (OMIM 257320) (Hong et
al., 2000). Al-Hassnan et al. (2011) suggested that RELN is the plausible major contributor to the facial anomalies and neurological abnormalities associated with chromosome 7q22-q23 deletions. Autism susceptibility locus 1 (AUTS1) (OMIM 209850) has been mapped to 7q22 and RELN,
LAMB1, IMMP2L and DOCK4 have been implicated as autism candidate genes (Bonora et al.,
2005; Cukier et al., 2009; Hutcheson et al., 2004; Maestrini et al., 2010; Skaar et al., 2005). The potential outcomes of the babies with haploinsufficiency of those genes after birth without prenatal detection are poor, and may be associated with neurological problems such as seizures, congenital contractures, mental retardation and autistic spectrum disorder in addition to facial cleft and genital abnormalities.
In summary, we present prenatal diagnosis and molecular cytogenetic characterization of de
novo interstitial deletion of 7q (7q22.1q31.1) in a fetus with an abnormal maternal serum screening result and ultrasound findings of facial cleft and hypogenitalism. We discuss the genotype-phenotype correlation and the consequence of haploinsufficiency of ZKSCAN5,
ARPC1A, CYP3A43, RELN, LAMB1, IMMP2L and DOCK4 in this case.
Acknowledgements
This work was supported by research grants NSC-99-2628-B-195-001-MY3 and NSC-101-2314-B-195-011-MY3 from the National Science Council and MMH-E-101-04 from Mackay Memorial Hospital, Taipei, Taiwan.
Appendix A. Supplementary data
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Figure Captions
Fig. 1. aCGH on uncultured amniocytesshows a 13.45-Mb deletion at chromosome 7q22.1-q31.1 [arr cgh 7q22.1.q31.1 (98,423,469-111,872,943)1] (NCBI build 37). (A) Chromosomal view and (B) zoom in view.
Fig. 2. The G-banded karyotype of 46,XY,del(7)(q22.1q31.1) shows an abnormal chromosome 7 [del(7)] with an interstitial deletion of 7q. The arrows indicate the breakpoints.
Fig. 3. Metaphase FISH analysis shows absence of the 7q31.1-specific probe signal (spectrum red) and presence of the 7q36.3-specific probe signal (spectrum green) on the aberrant chromosome 7 [del(7)]. The normal chromosome 7 contains both red and green signals.
Fig. 4. QF-PCR assays show absence of the maternal allele in the informative markers of D7S818 (7q22.1), D7S1799 (7q22.1) and D7S1817 (7q31.1). The deleted chromosome is from maternal origin.
Appendix A. Supplementary data
Fig. S1.The fetus at birth shows (A) facial dysmorphism of median cleft lip and palate and (B) micropenis and cryptorchidism.
