Rapid aneuploidy diagnosis by multiplex ligation-dependent probe amplification and array comparative genomic hybridization in pregnancy with major congenital malformations

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Case Report

Rapid aneuploidy diagnosis by multiplex ligation-dependent probe

amplification and array comparative genomic hybridization in pregnancy

with major congenital malformations

Chih-Ping Chen

a,b,c,d,e,f,

*

, Yi-Ning Su

g

, Shin-Yu Lin

h

, Chih-Long Chang

a

,

Yeou-Lih Wang

a

, Jiau-Pei Huang

a

, Chen-Yu Chen

a

, Fang-Yu Hung

i

,

Yi-Yung Chen

a

, Pei-Chen Wu

a

, Wayseen Wang

b,j

a

Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan b

Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan c_{Department of Biotechnology, Asia University, Taichung, Taiwan}

d_{School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan} e_{Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan} f_{Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan}

g_{Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan} h_{Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan} i_{Department of Obstetrics and Gynecology, Hsin Chu Mackay Memorial Hospital, Hsinchu, Taiwan}

j_{Department of Bioengineering, Tatung University, Taipei, Taiwan} Accepted 21 May 2010

Abstract

Objective: To report five cases of major congenital malformations associated with common aneuploidies detected by rapid aneuploidy diagnosis. Case Reports: The fetus in the first case presented cebocephaly, semilobar holoprosencephaly, and tetralogy of Fallot on ultrasound at 25 gestational weeks. Cordocentesis using multiplex ligation-dependent probe amplification to detect aneuploidies of chromosomes X, Y, 13, 18, and 21 in uncultured cord blood revealed three copies of all targets on chromosome 13 consistent with the diagnosis of trisomy 13. The fetus in the second case presented bilateral choroid plexus cysts, congenital diaphragmatic hernia, and club foot on ultrasound at 18 gestational weeks. Amniocentesis using array-based comparative genomic hybridization (aCGH) in uncultured amniocytes revealed a gain in the DNA dosage of chromosome 18 consistent with the diagnosis of trisomy 18. The fetus in the third case presented aortic stenosis and nuchal edema on ultrasound at 22 gestational weeks. Amniocentesis using aCGH in uncultured amniocytes revealed a result of monosomy X and Turner syndrome. The fetus in the fourth case presented nuchal cystic hygroma and ventriculomegaly on ultrasound at 17 gestational weeks. Amniocentesis using aCGH in uncultured amniocytes revealed a gain in the DNA dosage of chromosome 21 consistent with the diagnosis of trisomy 21. The fetus in the fifth case presented holoprosencephaly, omphalocele, and hydronephrosis on ultrasound at 17 gestational weeks. Amniocentesis using aCGH in uncultured amniocytes revealed a gain in the DNA dosage of chromosome 13 consistent with the diagnosis of trisomy 13.

Conclusions: Prenatal diagnosis of major congenital malformations should alert one to the possibility of chromosomal abnormalities. Multiplex ligation-dependent probe amplification and aCGH have the advantage of rapid aneuploidy diagnosis of common aneuploidies in cases with major congenital malformations.

Keywords: Array-based comparative genomic hybridization (aCGH); Multiplex ligation-dependent probe amplification (MLPA); Rapid aneuploidy diagnosis

* Corresponding author. Department of Obstetrics and Gynecology, Mackay Memorial Hospital, 92, Section 2, Chung-Shan North Road, Taipei, Taiwan. E-mail address:[email protected](C.-P. Chen).

Available online at www.sciencedirect.com

Taiwanese Journal of Obstetrics & Gynecology 50 (2011) 85e94

www.tjog-online.com

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Introduction

Rapid aneuploidy diagnosis (RAD) refers to the applica-tions of molecular cytogenetic techniques such as interphase fluorescence in situ hybridization, quantitative fluorescent polymerase chain reaction, multiplex ligation-dependent probe amplification (MLPA), and array-based comparative genomic hybridization (aCGH) for rapid prenatal diagnosis of common

aneuploidies[1]. Common aneuploidies, such as trisomies 13,

18 and 21, Turner syndrome (45,X), Klinefelter syndrome (47,XXY), triple X (47,XXX), 47,XYY, and triploidy account for more than 80% of significant chromosomal abnormalities

diagnosed in the prenatal period [1]. Other chromosomal

aberrations, such as balanced and unbalanced translocations, deletions, duplications, inversions, isochromosomes, and marker chromosomes account for only a small part of prena-tally detected chromosomal abnormalities. Here, we present

our experience of RAD by MLPA and aCGH in pregnancy with major congenital malformations.

Case reports Case 1

A 26-year-old primigravid woman underwent cordocentesis at 25 gestational weeks because of congenital malformation of the fetal brain. Prenatal ultrasound at 25 gestational weeks revealed cebocephaly with a single nostril, semilobar hol-oprosencephaly (HPE), and tetralogy of Fallot (Fig. 1). About 2 mL blood was aspired, of which 1 mL of blood was applied for MLPA using SALSA MLPA P095 aneuploidy kit (MRC-Holland bv, Amsterdam, The Netherlands) to detect aneuploidies of chromosomes X, Y, 13, 18, and 21, and 1 mL of blood was applied for conventional cytogenetic analysis.

Fig. 1. Prenatal ultrasound of Case 1 at 25 gestational weeks shows cebocephaly with a single nostril (arrow) on (A) three-dimensional ultrasound, (B) two-dimensional ultrasound, and (C) semilobar holoprosencephaly.

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Fig. 2. Multiplex ligation-dependent probe amplification in Case 1 shows a male fetus with three copies of all targets on chromosome 13 consistent with the diagnosis of trisomy 13. The wild type in a normal male control has two copies of all targets on chromosome 13. Arrows indicate chromosome 13 targets. WT¼wild type; ANEU ¼ aneuploidy test; ANEU-024 ¼ Case 1; ANEU-WT ¼wild type (control).

87 C.-P. Chen et al. / Taiwanese Journal of Obstetrics & Gynecology 50 (2011) 85e94

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Within 2 days, MLPA showed the result of a male fetus with three copies of all targets on chromosome 13, two copies of all targets for chromosomes 18 and 21, and one copy of all targets for the X and Y chromosomes within the P095 kit [mlpa

X,Y (P095) 1, 13 (P095) 3, 18,21 (P095) 2] (Fig. 2),

consistent with the diagnosis of trisomy 13. Conventional

cytogenetic analysis revealed a karyotype of 47,XY,þ13. The

parents decided to terminate the pregnancy. Case 2

A 39-year-old, gravida 3, para 2, woman underwent amniocentesis at 18 gestational weeks because of advanced maternal age. Prenatal ultrasound before amniocentesis revealed bilateral choroid plexus cysts, congenital diaphrag-matic hernia (CDH), and club foot. The fetal biometry was equivalent to 17 weeks. About 32 mL amniotic fluid was aspired, of which 15 mL of amniotic fluid was applied for aCGH using uncultured amniocytes, and 15 mL was applied for conventional cytogenetic analysis using cultured amniocytes. Within 3 days, bacterial artificial chromosome (BAC)-based aCGH showed the result of trisomy 18 [arr cgh

18p11.32q23 (RP11-1150C18/ RP11-87C15) 3] (Fig. 3).

Eleven days after amniocentesis, conventional cytogenetic

analysis revealed a karyotype of 47,XX,þ18. The parents

decided to continue the pregnancy. Prenatal ultrasound at 34 gestational weeks revealed polyhydramnios and a malformed fetus with intrauterine growth restriction, single umbilical artery, a flat facial profile, micrognathia, CDH, club feet, clenched hands, and a ventricular septal defect (Fig. 4).

Case 3

A 29-year-old, gravida 4, para 1, woman underwent amniocentesis at 23 gestational weeks because of fetal congenital anomalies. Prenatal ultrasound at 22 gestational weeks revealed aortic stenosis (AS) with a thickened aortic valve and a turbulent jet in the ascending aorta, and nuchal

edema with a thick nuchal fold of 0.95 cm (Fig. 5). About

38 mL amniotic fluid was aspired, of which 20 mL of amniotic fluid was applied for aCGH using uncultured amniocytes, and 15 mL was applied for conventional cytogenetic analysis using cultured amniocytes. Within 3 days, BAC-based aCGH showed the result of monosomy X [arr cgh 1-22 (2,853

BAC) 2, X (158 BAC) 1, Y (27 BAC) 0] (Fig. 6). Ten

days after amniocentesis, conventional cytogenetic analysis revealed a karyotype of 45,X. The parents decided to terminate the pregnancy. The parental karyotypes were normal. Case 4

A 37-year-old, gravida 5, para 3, woman underwent amnio-centesis at 18 gestational weeks because of advanced maternal age and fetal congenital anomalies. Prenatal ultrasound at 17 gestational weeks revealed ventriculomegaly and nuchal cystic hygroma (Fig. 7). About 36 mL amniotic fluid was aspired, of which 20 mL of amniotic fluid was applied for aCGH using uncultured amniocytes, and 15 mL was applied for conventional cytogenetic analysis using cultured amniocytes. Within 3 days, BAC-based aCGH showed the result of trisomy 21 [arr cgh

21p11.2q22.3 (RP11-430M17/ RP11-1000I21) 3] (Fig. 8).

Fig. 3. Bacterial artificial chromosomeebased array comparative genomic hybridization in Case 2 shows a duplication of chromosome 18 consistent with the diagnosis of trisomy 18.

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Ten days after amniocentesis, conventional cytogenetic analysis

revealed a karyotype of 47,XY,þ21. The parents decided to

terminate the pregnancy. Case 5

A 37-year-old, gravida 2, para 1, woman underwent amnio-centesis at 17 gestational weeks because of advanced maternal age and fetal congenital anomalies. Prenatal ultrasound at 17 gestational weeks revealed alobar HPE, mild hydronephrosis, and a small omphalocele containing the bowel (Fig. 9). About 38 mL amniotic fluid was aspired, of which 20 mL of amniotic fluid was applied for aCGH using uncultured amniocytes, and 17 mL was applied for conventional cytogenetic analysis using

cultured amniocytes. Within 3 days, BAC-based aCGH showed the result of trisomy 13 [arr cgh 13q11q34

(RP11-631L24/ RP11-450H16) 3] (Fig. 11). Ten days after

amniocentesis, conventional cytogenetic analysis revealed

a karyotype of 47,XY,þ13. The pregnancy was subsequently

terminated, and a 146-g fetus was delivered with premaxillary agenesis, omphalocele, and polydactyly of both feet (Fig. 10). Discussion

MLPA, first described by Schouten et al[2], is a molecular method to detect gene dosage abnormalities in a wide range of conditions by relative quantification of up to 45 DNA target sequences in one polymerase chain reaction with the input of Fig. 4. Prenatal ultrasound of Case 2 at 34 gestational weeks shows (A) a clenched hand, (B) a club foot, (C) congenital diaphragmatic hernia with a stomach (S) in the chest and a heart (H) with a ventricular septal defect (arrow), and (D) a flat face with micrognathia.

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20 ng or more DNA, but without the requirement of living cells or cell cultures. It can be automated and can obtain the

result as quickly as 30 hours [3]. In MLPA, it is the probes

added to the samples that are amplified and quantified[4]. The

MLPA kit for RAD is commercially available. For the SALSA MLPA P095 aneuploidy kit, eight target sequences are chosen for each of the chromosomes 13, 18, 21, and X, and four target sequences are chosen for the chromosome Y. MLPA can Fig. 5. Prenatal ultrasound of Case 3 at 22 gestational weeks shows (A) nuchal edema with a thick nuchal fold of 0.95 cm and (B) aortic stenosis with a thickened aortic valve and a turbulent jet (yellow color) in the ascending aorta. AO¼ ascending aorta; LV ¼ left ventricle; RV ¼ right ventricle.

Fig. 6. Bacterial artificial chromosomeebased array comparative genomic hybridization in Case 3 shows monosomy X consistent with the diagnosis of Turner syndrome.

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Fig. 7. Prenatal ultrasound of Case 4 at 17 gestational weeks shows (A) bilateral ventriculomegaly and (B) nuchal cystic hygroma.

Fig. 8. Bacterial artificial chromosomeebased array comparative genomic hybridization in Case 4 shows a duplication of chromosome 21 consistent with the diagnosis of trisomy 21.

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reliably determine common aneuploidies. The diagnostic accuracy of MLPA for detecting common aneuploidies of chromosomes X, Y, 13, 18, and 21 is comparable with that of

karyotyping [3,5e12]. Compared with conventional

kar-yotyping, MLPA has the advantages of sparing the waiting time and reducing the cost, but the disadvantages of an inability to detect structural chromosomal abnormalities, maternal cell contamination, and triploidy[1,13]. It has been reported that MLPA is not expected to detect chromosome

mosaicism [6,8]. However, in a prospective study of 4,000

amniotic fluid samples, Van Opstal et al[3]was able to detect some mosaic cases, structural chromosome aberrations, and male fetuses with triploidy by calculating the cutoff values for all the probes in the P095 MLPA kit and comparing the relative probe signals with the normal cutoff values.

BAC-based and oligonucleotide-based aCGH are compre-hensive and high-resolution genome-wide screening methods to obtain DNA copy number information in a single rapid measurement without the requirement of living cells or cell

cultures [1,13]. aCGH has the ability to detect DNA dosage

imbalance including deletions and duplications and the inability to detect very low-level mosaicism, balanced trans-locations, inversions, and polyploidy. aCGH has proven to be invaluable for RAD of unbalanced chromosomal abnormalities

in uncultured amniocytes[14]. Recent studies have suggested

that aCGH can detect as little as 20% (and possibly 10%) mosaicism for the peripheral blood[15,16].

Our Case 1 was associated with HPE and cebocephaly. In this case, the facial dysmorphism of a single nostril was evident by two- and three-dimensional prenatal ultrasound.

Chen et al [17] previously described the dysmorphism of

a prominent nose and a large common nasal cavity in a trisomy 13 fetus with cebocephaly. Cytogenetic abnormali-ties have been reported in 24e45% of live births with HPE

[18e20]. In a meta-analysis of chromosomal abnormalities

associated with HPE, Blaas et al [21] suggested that the

frequency was 34.7% (92/265) or more. Reported chromo-somal abnormalities associated with HPE include trisomy 13, trisomy 18, triploidy, del(2p), dup(3p), del(7q), del(13q), del

(18p), del(21q), and interstitial deletion of 14q13 [22,23].

Several new submicroscopic rearrangements have been iden-tified by aCGH in HPE cases such as interstitial deletions of 1p, 6q, 10p, 16p, 18q, 20p, 21q, and Xp, and subtelomeric deletions in 19pter and 6qter[24]. HPE can be a first-trimester sonographic feature of fetuses in trisomy 13 pregnancies[25]. HPE has been found in 26.5% (48/181) of trisomy 13 fetuses in the first trimester[26]. In a meta-analysis of fetal trisomy 13

diagnosed in the second and third trimesters, Chen[25]found

the mean frequency of HPE in trisomy 13 was 27% (64/237).

Our Case 2 was associated with CDH. Snijders et al [27]

found that CDH was diagnosed in 10% of fetuses with trisomy 18. CDH can be associated with chromosomal abnormalities

[28]. Trisomies 13, 18, and 21, and 45,X are the most common

aneuploidies associated with CDH[29e31]. Frequently

repor-ted structural chromosomal abnormalities associarepor-ted with CDH include tetrasomy 12p (Pallister-Killian syndrome), del(15) (q26.1eq26.2), del(8)(p23.1), cytogenetic rearrangements of

8q23, del(4)(p16), þder(22) t(11;22)(q23;q11), and del(1)

(q41eq42.12) [30e33]. Other reported chromosomal

rear-rangements associated with CDH include duplication of 1q25eq31.2, deletion or duplication of 2q37, deletion of 3q22, deletion or duplication of 4q31, deletion of 5p15, deletion of 6p25, deletion of 6q25.3-qter, duplication of 8p21ep23.1, deletion of 8q22eq23, deletion of 9p24-pter, deletion of 11p13, duplication of 11q23.3-qter, duplication of 12p and duplication of 14q32[31]. CDH has been seen in patients with tetrasomy 21, trisomy 22, and trisomy 9[30,34,35].

Our Case 3 was associated with AS with nuchal edema.

Snijders et al[27]found that nuchal edema was diagnosed in

6% of fetuses with Turner syndrome. About one-third of fetuses with nuchal edema have chromosomal abnormalities,

mainly trisomies 21, 18, and 13 [28]. Song et al [36]found

Fig. 10. (A) A trisomy 13 fetus with premaxillary agenesis, omphalocele, and polydactyly of feet. (B) Polydactyly of both feet.

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chromosomal abnormality in 11.1% (1/9) of the fetuses with AS. In a study of 179 patients with Turner syndrome,

Gøtzsche et al [37] found that 46 (25.7%) patients had

cardiovascular malformations, 33 (18.4%) patients had aortic valve abnormalities, and 18 (10.1%) patients had aortic coarctation. Prandstraller et al [38] found that patients with

Turner syndrome had a higher prevalence (29/136¼ 21.3%) of

congenital heart defects than the general population (21.3% vs.

0.8%, 27 times more frequent). Prandstraller et al[38]found

that among the congenital heart defects, partial anomalous pulmonary venous return appeared to be the most prevalent

anomaly (4/136 ¼ 2.9%) (2.9% vs. 0.009%, 322 times more

frequent) followed by aortic valve disease (AS and/or

incompetence) (7/136 ¼ 5.1%) (5.1% vs. 0.035%, 146 times

more frequent) and aortic coarctation (6/136 ¼ 4.4%) (4.4%

vs. 0.043%, 102 times more frequent).

Our Case 4 was associated with ventriculomegaly and

nuchal cystic hygroma. Snijders et al [27] found that

ven-triculomegaly was diagnosed in 16% of fetuses with trisomy 21. Ventriculomegaly can be associated with chromosomal

abnormalities [23]. Snijders et al[27] reported chromosomal

abnormalities in 13% of fetuses with prenatally detected ventriculomegaly, and trisomies 18, 13, and 21 and triploidy are the most common aneuploidies associated with

ven-triculomegaly. Snijders et al [27] found that cystic hygroma

was diagnosed in 1% of fetuses with trisomy 21. Cystic hygroma can be associated with chromosomal abnormalities

[28]. Snijders et al [27]reported chromosomal abnormalities

in 68% of fetuses with prenatally detected cystic hygroma, and

Turner syndrome, trisomy 21, and trisomy 18 are the most common aneuploidies associated with cystic hygroma.

Our Case 5 was associated with HPE, omphalocele, mild hydronephrosis, and polydactyly. Snijders et al[27]found that omphalocele was diagnosed in 17% of fetuses with trisomy 13.

Snijders et al[27]reported chromosomal abnormalities in 35%

of fetuses with prenatally detected omphalocele, and trisomies 18 and 13 are the most common aneuploidies. Snijders et al

[27]found that mild hydronephrosis was diagnosed in 37% of

fetuses with trisomy 13. The reported frequencies of poly-dactyly in fetuses with trisomy 13 range from 7.1% to 21.2%

[28].

In conclusion, prenatal diagnosis of major congenital malformations should alert one to the possibility of chromo-somal abnormalities. MLPA and aCGH have the advantage of RAD of common aneuploidies in cases with major congenital malformations.

Acknowledgments

This work was supported by research grants NSC-96-2314-B-195-008-MY3 and NSC-97-2314-B-195-006-MY3 from the National Science Council, and MMH-E-99004 from Mackay Memorial Hospital, Taipei, Taiwan.

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Fig. 11. Bacterial artificial chromosome-based array comparative genomic hybridization in Case 5 shows a duplication of chromosome 13 consistent with the diagnosis of trisomy 13.

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