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Karyotype versus genomic hybridization for the prenatal diagnosis of chromosomal abnormalities: a metaanalysis Wilmar Saldarriaga, MD, MSc; Herney Andre´s Garcı´a-Perdomo, MD, MSc, EdD, PhD; Johanna Arango-Pineda, MD; Javier Fonseca, MD, MSc OBJECTIVE: The aim of this study was to determine the diagnostic accuracy of comparative genomic hybridization (CGH) compared with karyotyping for the detection of numerical and structural chromosomal alterations in prenatal diagnosis. STUDY DESIGN: A metaanalysis was performed using searches of
PubMed, EMBASE, CENTRAL, Cochrane Register of Diagnostic Test Accuracy Studies, Google Scholar, gray literature, and reference manuals. No language restriction was imposed. We included cross-sectional, cohort, and case-control studies published from January 1980 through March 2014 in the analysis. Studies of pregnant women who received chorionic villus biopsies, amniocentesis, or cordocentesis and then underwent CGH and karyotype analysis were included. Two independent reviewers assessed each study by title, abstract, and full text before its inclusion in the analysis. Methodological quality was assessed using QUADAS2, and a third reviewer resolved any disagreement. Conclusions were obtained through tests (sensitivity, specificity, and likelihood ratios) for the presence of numerical and structural chromosomal abnormalities. The reference used for these calculations was the presence of any abnormalities in either of the 2 tests (karyotype or CGH), although it should be noted that in most cases, the karyotyping test had a lower yield compared with CGH. Statistical analysis was performed in RevMan 5.2 and the OpenMeta[Analyst] program.
RESULTS: In all, 137 articles were found, and 6 were selected for inclusion in the systematic review. Five were included in the metaanalysis. According to the QUADAS2 analysis of methodology quality, there is an unclear risk for selection bias and reference and standard tests. In the other elements (flow, time, and applicability conditions), a low risk of bias was found. CGH findings were as follows: sensitivity 0.939 (95% confidence interval [CI], 0.838e0.979), I2 ¼ 82%; specificity 0.999 (95% CI, 0.998e1.000), I2 ¼ 0%; negative likelihood ratio 0.050 (95% CI, 0.015e0.173), I2 ¼ 0%; and positive likelihood ratio 1346.123 (95% CI, 389e4649), I2 ¼ 0%. Karyotype findings were as follows: sensitivity 0.626 (95% CI, 0.408e0.802), I2 ¼ 93%; specificity 0.999 (95% CI, 0.998e1.000), I2 ¼ 0%; negative likelihood ratio 0.351 (95% CI, 0.101e1.220), I2 ¼ 0%; and positive likelihood ratio 841 (95% CI, 226e3128), I2 ¼ 10%. CONCLUSION: This systematic review provides evidence of the relative advantage of using CGH in the prenatal diagnosis of chromosomal and structural abnormalities over karyotyping, demonstrating significantly higher sensitivity with similar specificity.
Key words: chromosomal abnormalities, comparative genomic hybridization, karyotype, prenatal diagnosis
Cite this article as: Saldarriaga W, Garcı´a-Perdomo HA, Arango-Pineda J, et al. Karyotype versus genomic hybridization for the prenatal diagnosis of chromosomal abnormalities: a metaanalysis. Am J Obstet Gynecol 2014;211:x.ex-x.ex.
P
renatal studies include the detection of numerical and structural chromosomal abnormalities. However, sampling of fetal genetic material requires the use of invasive procedures that
pose risks for both the mother and child.1 For this reason, a series of screening tests is performed prior to fetal chromosomal analysis to determine if there is a probability 1% of finding a
From the Departments of Obstetrics and Gynecology (Drs Saldarriaga, Fonseca, and ArangoPineda), Urology (Dr García-Perdomo), and Morphology (Dr Saldarriaga), School of Medicine, University of Valle, Cali, Colombia. Received July 9, 2014; revised Aug. 19, 2014; accepted Oct. 3, 2014. The authors report no conflict of interest. Presented at the 29th Annual Scientific Meeting of the Colombian Obstetrical and Gynecologic Society, Medellin, Colombia, May 28-31, 2014. Corresponding author: Herney Andrés García-Perdomo, MD, MSc, EdD, PhD. Herney.garcia@ correounivalle.edu.co 0002-9378/$36.00 ª 2014 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.ajog.2014.10.011
chromosomal abnormality. Parameters such as maternal age, biochemical test results, and ultrasound markers, such as fetal anatomy defects, justify performing the more invasive procedure.2 The most common diagnostic test for chromosomal abnormalities is G-banding karyotyping. Other tests include fluorescent in situ hybridization (FISH) or quantitative fluorescent polymerase chain reaction. Karyotyping can detect numerical chromosomal abnormalities in chromosomes as well as structural changes, such as the loss or gain of upwards of 5 megabases of genetic material. Other techniques detect common trisomies and monosomies (13, 18, 21, X,
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ajog.org bases that are not detected by karyotype. In 2010, a consensus document4 and an economic analysis5 were published that suggested that CGH should be considered the first diagnostic test, replacing karyotyping in patients with neurological problems, autism, and cognitive deficits and in newborns with congenital anomalies of unknown etiology. In prenatal diagnosis, studies comparing different chromosomal alteration analysis techniques in high-risk patients report diagnostic frequencies between 2.5-4.2% with karyotyping,6 whereas frequencies of 5.3-15% have been reported with CGH.7-10 The detection increases significantly for CGH (9.3-39%) when fetal anatomic defects are indicated.8,9,11 The patient is not subjected to additional risk, and results are obtained more rapidly. However, there is an increase in the cost as well as the probability of finding variants of an uncertain nature.7,10 Given the advantages of CGH over karyotyping in prenatal diagnosis, the use of this molecular test has increased in countries where the additional cost is borne by health insurance as well as in countries or states where abortion is permitted. So far, there was only 1 metaanalysis12 suggesting that CGH increases the detection rate to diagnose chromosomal abnormalities for prenatal indications overall. That metaanalysis focused on the agreement between both tools and the detection rate of chromosomal abnormalities, however it was not related to diagnostic accuracy. The aim of this study was to determine the diagnostic accuracy of CGH and karyotyping compared with the sum of the results of the 2 tests for the detection of numerical and structural chromosomal abnormalities in prenatal diagnosis.
FIGURE 1
Flowchart
CGH, comparative genomic hybridization. Saldarriaga. Karyotype vs genomic hybridization for the prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
and Y), in addition to fetal chromosomal sex, but do not diagnose structural alterations.3 The aforementioned tests are techniques often combined with karyotyping because results are available in approximately a week, whereas karyotyping requires 2-3 weeks.
Comparative genomic hybridization (CGH) has emerged as a molecular test for chromosomal analysis and it is used in prenatal diagnosis, pediatric patients, or adults with specific indications. CGH detects microdeletions and microduplications sizing upwards of 500 pair-
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This study was conducted according to the recommendations of the Cochrane Collaboration and is reported following the PRISMA Statement. The protocol was registered in the international prospective register of systematic reviews (PROSPERO): CRD42014007627. We designed a search strategy for studies published in MEDLINE via
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TABLE 1
Characteristics of included studies Sample size, n
Study
Country
Array type
Sample type
Array indication
Van den Veyver et al17 (2009), prospective (cross-sectional)
United States
BAC chromosomal microarray V5 or 6; V6 of BCM oligonucleotide chromosomal microarray
AF 254, CVS 53
Advanced maternal age (33.5%), abnormal ultrasound finding (22.9%), family history of genetic disease (23.7%), abnormal fetal karyotype (7.6%), parental anxiety (9%), altered serum screening (2.5%), others (0.9%)
309
Maya et al15 (2010), retrospective (cross-sectional)
Israel
BAC using SignatureChip whole genome or oligonucleotide microarrays
AF 243, CVS 16
Advanced maternal age (22.7%), abnormal ultrasound finding (38%), familial congenital disease (16%), abnormal fetal karyotype (5.6%), parental anxiety (17%), altered serum screening (0.7%)
269
Fiorentino et al14 (2011), prospective (cross-sectional)
Italy
Whole-genome BAC microarrayseCytoChip Focus Constitutional
AF 938, CVS 99
Advanced maternal age 42.8%), altered serum screening (1.3%), abnormal ultrasound (4.6%), abnormal fetal karyotype (0.8%), family history of genetic disease (1.1%), parental anxiety (46.8%), others (2.4%)
1037
Wapner et al16 (2012), prospective (cross-sectional)
United States
Agilent 4-plex array and Affymetrix genomewide human SNP array 6.0
AF 1627, CVS 1910
Abnormal ultrasound finding (25.8%), advanced maternal age (47.9%), altered serum screening (19.3%), others (9.7%)
4282
Lee et al11 (2012), prospective (cross-sectional)
Taiwan
1-Mb resolution BAC from 2010, until 60-K oligonucleotide
AF 2926, CVS 82, fetal blood 93
Abnormal ultrasound findings (6.1%), altered serum screening (0.8%), advanced maternal age (60.2%), parental anxiety (31.1%)
3171
Armengol et al7 (2012), prospective
Spain
Not defined
AF 728, CVS 164, fetal blood 14
Abnormal ultrasound finding (19%), altered serum screening (25.9%), history of congenital disease (16%), advanced maternal age (30.1%), parental anxiety (6.6%), other (2.2%)
906
AF, amniotic fluid; AMA, advanced maternal age (35 years old); BAC, bacterial artificial chromosome; CVS, chorionic villus sampling; SNP, single nucleotide polymorphism. Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
PubMed, CENTRAL, Cochrane Register of Diagnostic Test Accuracy Studies, and EMBASE. The search strategy was specific for each database and included a combination of the medical subject headings and free-text terms for “comparative genomic hybridization” and “karyotype.” No language or publication status restrictions were imposed. We included articles from Jan. 1, 1980, through March 31, 2014. The full search strategies are listed in the Appendix. Other electronic sources were used to find additional studies, such as conference abstracts, Google Scholar, DARE, and PROSPERO. We looked for additional studies in the reference lists of selected articles and contacted authors about their
knowledge of published or unpublished articles. The results of searches were crosschecked to eliminate duplicates.
Eligibility criteria Studies We included cross-sectional, case-control, and cohort studies conducted from Jan. 1, 1980, through March 31, 2014. No language restrictions were imposed. Studies were required to report at least sensitivity and specificity or data to calculate these parameters. Participants Pregnant women who underwent chorionic villus sampling, amniocentesis, or cordocentesis to perform CGH and karyotyping.
There were no preferences with respect to any other demographic characteristics of the participants. Comparisons We intended to perform the following comparisons: Karyotype (reference standard) vs CGH (index test). Karyotype plus CGH vs karyotype. Karyotype plus CGH vs CGH. However, at the time of analysis, we determined that CGH diagnosed abnormalities that the karyotype did not. Therefore, we decided to create a reference standard according to the literature (karyotype þ CGH).
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FIGURE 2
Risk of bias within studies
Data collection process Relevant data were collected using a standardized data extraction sheet, which contained the following: study design, methods, participants, index test, standard of reference, and final outcome details. Reviewers confirmed all data entries and checked the entries at least twice for completeness and accuracy. If some information was missing, we contacted the authors to obtain the complete data.
Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
Outcomes Outcomes were sensitivity, specificity, and likelihood ratios for numeric and structural chromosomal abnormalities.
Exclusions We excluded studies using karyotype or CGH independently, and those in which data were unavailable to obtain sensitivity and specificity.
Study selection Two investigators (H.A.G-P., J.A-P.) independently and blindly screened the titles and abstracts to determine the potential usefulness of the articles. Two assessors (H.A.G-P., J.A-P.) applied eligibility criteria to the full-text articles during the final selection. When discrepancies occurred, a final decision was reached by consensus. If the 2 assessors
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FIGURE 3
Risk of bias across studies
Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
Risk of bias in and across individual studies The risk of bias was assessed independently by at least 2 researchers (H.A.GP., J.A-P.) using the QUADAS2 tool, which evaluates items related to the patient selection, the index and reference tests, the flow and timing, and the concerns about their applicability. We solved disagreements by consensus. The risk of bias table (within and across studies) was edited using Review Manager Software version 5.2 (RevMan; Cochrane Collaboration, Oxford, England) to illustrate the judgments for each study. Summary measures Analyses were performed in RevMan 5.2, OpenMeta[Analyst] (http://www.cebm. brown.edu/open_meta), and Stata 10 (StataCorp, College Station, TX) as needed. The sensitivity, specificity, likelihood ratios, and diagnostic odds ratios were measured for comparisons with 95% confidence intervals (CIs). We performed fixed effects or random effect metaanalysis according to the heterogeneity or homogeneity among the studies. We also performed forest plots and summary receiver operating characteristic for comparisons. Heterogeneity between trials was assessed through the I2 statistic. A value 50% can represent heterogeneity according to Higgins and Green13 (2011). We also intended to analyze heterogeneity according to the following: reference standard, clinical spectrum, type of method used, and age of the patient.
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FIGURE 4
CGH vs gold standard (CGH D karyotype): sensitivity and specificity forest plot
CGH, comparative genomic hybridization. Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
Additional analyses We intended to perform the following subgroup analysis: low- and high-risk pregnancies, history of chromosomal abnormalities, parents with chromosomal abnormalities, maternal age >37 years, biochemical screening plus maternal ultrasonography, and abnormalities detected on ultrasonography. However, the studies lacked sufficient data to perform these types of analyses. Sensitivity analysis We undertook a sensitivity analysis based on unknown significance variables considered important for analysis and results. Publication bias Publication bias was not assessed due to the number of studies found (1000 cases and review of the literature. Prenat Diagn 2012;32:351-61. 10. Shaffer LG, Dabell MP, Fisher AJ, et al. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn 2012;32: 976-85. 11. Lee C-N, Lin S-Y, Lin C-H, Shih J-C, Lin TH, Su Y-N. Clinical utility of array comparative genomic hybridization for prenatal diagnosis: a cohort study of 3171 pregnancies; editorial comment. BJOG 2012;119:614-25.
12. Hillman SC, Pretlove S, Coomarasamy A, et al. Additional information from array comparative genomic hybridization technology over conventional karyotyping in prenatal diagnosis: a systematic review and meta-analysis. Ultrasound Obstet Gynecol 2011;37:6-14. 13. Higgins J, Green S. Cochrane Handbook for Systematic Reviews of Interventions version 5.1. 0. The Cochrane Collaboration; 2011. Available at: www.cochrane-handbook.org. Accessed Jan. 15, 2014. 14. Fiorentino F, Caiazzo F, Napolitano S, et al. Introducing array comparative genomic hybridization into routine prenatal diagnosis practice: a prospective study on over 1000 consecutive clinical cases. Prenat Diagn 2011;31:1270-82. 15. Maya I, Davidov B, Gershovitz L, et al. Diagnostic utility of array-based comparative genomic hybridization (aCGH) in a prenatal setting. Prenat Diagn 2010;30:1131-7. 16. Wapner RJ, Martin CL, Levy B, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012;367: 2175-84. 17. Van den Veyver IB, Patel A, Shaw CA, et al. Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases. Prenat Diagn 2009;29:29-39. 18. American College of Obstetricians and Gynecologists. Array comparative genomic hybridization in prenatal diagnosis. ACOG Committee opinion no. 446. Obstet Gynecol 2009;114:1161-3. 19. Mansfield ES. Diagnosis of Down syndrome and other aneuploidies using quantitative polymerase chain reaction and small tandem repeat polymorphisms. Hum Mol Genet 1993;2:43-50. 20. Pertl B, Kopp S, Kroisel P, Tului L, Brambati B, Adinolfi M. Rapid detection of chromosome aneuploidies by quantitative fluorescence PCR: first application on 247 chorionic villus samples. J Med Genet 1999;36:300-3. 21. Schouten JP. Relative quantification of 40 nucleic acid sequences by multiplex ligationdependent probe amplification. Nucleic Acids Res 2002;30:e57. 22. Beaudet AL. Ethical issues raised by common copy number variants and single nucleotide polymorphisms of certain and uncertain significance in general medical practice. Genome Med 2010;2:42. 23. Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 2007;39(Suppl):S48-54. 24. Riggs ER, Church DM, Hanson K, et al. Towards an evidence-based process for the clinical interpretation of copy number variation. Clin Genet 2012;81:403-12. 25. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet 2004;36:949-51. 26. Giardino D, Corti C, Ballarati L, et al. De novo balanced chromosome rearrangements in prenatal diagnosis. Prenat Diagn 2009;29: 257-65.
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27. De Gregori M, Ciccone R, Magini P, et al. Cryptic deletions are a common finding in “balanced” reciprocal and complex chromosome rearrangements: a study of 59 patients. J Med Genet 2007;44:750-62. 28. Schluth-Bolard C, Delobel B, Sanlaville D, et al. Cryptic genomic imbalances in de novo and inherited apparently balanced chromosomal rearrangements: array CGH study of 47 unrelated cases. Eur J Med Genet 2009;52: 291-6. 29. Brady PD, Vermeesch JR. Genomic microarrays: a technology overview. Prenat Diagn 2012;32:336-43.
A PPENDIX Search strategies Search strategy for MEDLINE via PubMed: (‘Comparative genomic hybridization’ [mh] OR ‘a-CGH’ [tw] OR aCGH [tw] OR CGH [tw]) AND (Karyotype [mh] OR caryotype [tw] OR ‘chromosomal arrangement’ [tw] OR ‘chromosomal configuration’ [tw] OR ‘chromosomal pattern’ [tw] OR ‘chromosome arrangement’ [tw] OR kariotype [tw] OR karotype [tw] OR karytype [tw]) AND (‘Prenatal diagnosis’ [mh] OR ‘Fetal aneuploidy’ [mh] OR ‘Maternal serum screening’ [mh] OR ‘Chromosomal anomalies’ [tw] OR ‘Chromosomal defects’ [tw]) AND (‘Diagnostic test, routine’ [mh] OR ‘Sensitivity and specificity’ [mh] OR ‘Roc curve’ [mh] OR ‘Predictive value of tests’ [mh] OR Sensitivity [tw] OR Specificity [tw] OR Accuracy [tw] OR ‘Predictive value’ [tw] OR Likelihood [tw]) Search strategy for EMBASE: (comparative genomic hybridization [Emtree] OR ‘a-CGH’ [tw] OR aCGH [tw] OR CGH [tw]) AND (Karyotype [Emtree] OR caryotype [tw] OR ‘chromosomal arrangement’ [tw] OR ‘chromosomal configuration’ [tw] OR ‘chromosomal pattern’ [tw] OR ‘chromosome arrangement’ [tw] OR kariotype [tw] OR karotype [tw] OR karytype [tw]) AND (Prenatal diagnosis [Emtree] OR aneuploidy [Emtree] OR maternal serum screening test [Emtree] OR chromosome aberration [Emtree]) AND (Diagnostic accuracy [Emtree] OR Sensitivity and specificity [Emtree] OR receiver operating characteristic
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[Emtree] OR Predictive value [Emtree] OR Likelihood [tw]) Search strategy for CENTRAL and Cochrane Register of Diagnostic Test Accuracy Studies: (‘Comparative genomic hybridization’ [mh] OR ‘a-CGH’ [tw] OR aCGH [tw] OR CGH [tw]) AND (Karyotype [mh] OR
ajog.org caryotype [tw] OR ‘chromosomal arrangement’ [tw] OR ‘chromosomal configuration’ [tw] OR ‘chromosomal pattern’ [tw] OR ‘chromosome arrangement’ [tw] OR kariotype [tw] OR karotype [tw] OR karytype [tw]) AND (‘Prenatal diagnosis’ [mh] OR ‘Fetal aneuploidy’ [mh] OR ‘Maternal serum screening’
[mh] OR ‘Chromosomal anomalies’ [tw] OR ‘Chromosomal defects’ [tw]) AND (‘Diagnostic test, routine’ [mh] OR ‘Sensitivity and specificity’ [mh] OR ‘Roc curve’ [mh] OR ‘Predictive value of tests’ [mh] OR Sensitivity [tw] OR Specificity [tw] OR Accuracy [tw] OR ‘Predictive value’ [tw] OR Likelihood [tw])
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Karyotype versus genomic hybridization for the prenatal diagnosis of chromosomal abnormalities: a metaanalysis Wilmar Saldarriaga, MD, MSc; Herney Andre´s Garcı´a-Perdomo, MD, MSc, EdD, PhD; Johanna Arango-Pineda, MD; Javier Fonseca, MD, MSc OBJECTIVE: The aim of this study was to determine the diagnostic accuracy of comparative genomic hybridization (CGH) compared with karyotyping for the detection of numerical and structural chromosomal alterations in prenatal diagnosis. STUDY DESIGN: A metaanalysis was performed using searches of
PubMed, EMBASE, CENTRAL, Cochrane Register of Diagnostic Test Accuracy Studies, Google Scholar, gray literature, and reference manuals. No language restriction was imposed. We included cross-sectional, cohort, and case-control studies published from January 1980 through March 2014 in the analysis. Studies of pregnant women who received chorionic villus biopsies, amniocentesis, or cordocentesis and then underwent CGH and karyotype analysis were included. Two independent reviewers assessed each study by title, abstract, and full text before its inclusion in the analysis. Methodological quality was assessed using QUADAS2, and a third reviewer resolved any disagreement. Conclusions were obtained through tests (sensitivity, specificity, and likelihood ratios) for the presence of numerical and structural chromosomal abnormalities. The reference used for these calculations was the presence of any abnormalities in either of the 2 tests (karyotype or CGH), although it should be noted that in most cases, the karyotyping test had a lower yield compared with CGH. Statistical analysis was performed in RevMan 5.2 and the OpenMeta[Analyst] program.
RESULTS: In all, 137 articles were found, and 6 were selected for inclusion in the systematic review. Five were included in the metaanalysis. According to the QUADAS2 analysis of methodology quality, there is an unclear risk for selection bias and reference and standard tests. In the other elements (flow, time, and applicability conditions), a low risk of bias was found. CGH findings were as follows: sensitivity 0.939 (95% confidence interval [CI], 0.838e0.979), I2 ¼ 82%; specificity 0.999 (95% CI, 0.998e1.000), I2 ¼ 0%; negative likelihood ratio 0.050 (95% CI, 0.015e0.173), I2 ¼ 0%; and positive likelihood ratio 1346.123 (95% CI, 389e4649), I2 ¼ 0%. Karyotype findings were as follows: sensitivity 0.626 (95% CI, 0.408e0.802), I2 ¼ 93%; specificity 0.999 (95% CI, 0.998e1.000), I2 ¼ 0%; negative likelihood ratio 0.351 (95% CI, 0.101e1.220), I2 ¼ 0%; and positive likelihood ratio 841 (95% CI, 226e3128), I2 ¼ 10%. CONCLUSION: This systematic review provides evidence of the relative advantage of using CGH in the prenatal diagnosis of chromosomal and structural abnormalities over karyotyping, demonstrating significantly higher sensitivity with similar specificity.
Key words: chromosomal abnormalities, comparative genomic hybridization, karyotype, prenatal diagnosis
Cite this article as: Saldarriaga W, Garcı´a-Perdomo HA, Arango-Pineda J, et al. Karyotype versus genomic hybridization for the prenatal diagnosis of chromosomal abnormalities: a metaanalysis. Am J Obstet Gynecol 2014;211:x.ex-x.ex.
P
renatal studies include the detection of numerical and structural chromosomal abnormalities. However, sampling of fetal genetic material requires the use of invasive procedures that
pose risks for both the mother and child.1 For this reason, a series of screening tests is performed prior to fetal chromosomal analysis to determine if there is a probability 1% of finding a
From the Departments of Obstetrics and Gynecology (Drs Saldarriaga, Fonseca, and ArangoPineda), Urology (Dr García-Perdomo), and Morphology (Dr Saldarriaga), School of Medicine, University of Valle, Cali, Colombia. Received July 9, 2014; revised Aug. 19, 2014; accepted Oct. 3, 2014. The authors report no conflict of interest. Presented at the 29th Annual Scientific Meeting of the Colombian Obstetrical and Gynecologic Society, Medellin, Colombia, May 28-31, 2014. Corresponding author: Herney Andrés García-Perdomo, MD, MSc, EdD, PhD. Herney.garcia@ correounivalle.edu.co 0002-9378/$36.00 ª 2014 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.ajog.2014.10.011
chromosomal abnormality. Parameters such as maternal age, biochemical test results, and ultrasound markers, such as fetal anatomy defects, justify performing the more invasive procedure.2 The most common diagnostic test for chromosomal abnormalities is G-banding karyotyping. Other tests include fluorescent in situ hybridization (FISH) or quantitative fluorescent polymerase chain reaction. Karyotyping can detect numerical chromosomal abnormalities in chromosomes as well as structural changes, such as the loss or gain of upwards of 5 megabases of genetic material. Other techniques detect common trisomies and monosomies (13, 18, 21, X,
MONTH 2014 American Journal of Obstetrics & Gynecology FLA 5.2.0 DTD YMOB10067_proof 28 October 2014 3:11 am ce
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ajog.org bases that are not detected by karyotype. In 2010, a consensus document4 and an economic analysis5 were published that suggested that CGH should be considered the first diagnostic test, replacing karyotyping in patients with neurological problems, autism, and cognitive deficits and in newborns with congenital anomalies of unknown etiology. In prenatal diagnosis, studies comparing different chromosomal alteration analysis techniques in high-risk patients report diagnostic frequencies between 2.5-4.2% with karyotyping,6 whereas frequencies of 5.3-15% have been reported with CGH.7-10 The detection increases significantly for CGH (9.3-39%) when fetal anatomic defects are indicated.8,9,11 The patient is not subjected to additional risk, and results are obtained more rapidly. However, there is an increase in the cost as well as the probability of finding variants of an uncertain nature.7,10 Given the advantages of CGH over karyotyping in prenatal diagnosis, the use of this molecular test has increased in countries where the additional cost is borne by health insurance as well as in countries or states where abortion is permitted. So far, there was only 1 metaanalysis12 suggesting that CGH increases the detection rate to diagnose chromosomal abnormalities for prenatal indications overall. That metaanalysis focused on the agreement between both tools and the detection rate of chromosomal abnormalities, however it was not related to diagnostic accuracy. The aim of this study was to determine the diagnostic accuracy of CGH and karyotyping compared with the sum of the results of the 2 tests for the detection of numerical and structural chromosomal abnormalities in prenatal diagnosis.
FIGURE 1
Flowchart
CGH, comparative genomic hybridization. Saldarriaga. Karyotype vs genomic hybridization for the prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
and Y), in addition to fetal chromosomal sex, but do not diagnose structural alterations.3 The aforementioned tests are techniques often combined with karyotyping because results are available in approximately a week, whereas karyotyping requires 2-3 weeks.
Comparative genomic hybridization (CGH) has emerged as a molecular test for chromosomal analysis and it is used in prenatal diagnosis, pediatric patients, or adults with specific indications. CGH detects microdeletions and microduplications sizing upwards of 500 pair-
M ATERIALS
AND
M ETHODS
This study was conducted according to the recommendations of the Cochrane Collaboration and is reported following the PRISMA Statement. The protocol was registered in the international prospective register of systematic reviews (PROSPERO): CRD42014007627. We designed a search strategy for studies published in MEDLINE via
1.e2 American Journal of Obstetrics & Gynecology MONTH 2014 FLA 5.2.0 DTD YMOB10067_proof 28 October 2014 3:11 am ce
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TABLE 1
Characteristics of included studies Sample size, n
Study
Country
Array type
Sample type
Array indication
Van den Veyver et al17 (2009), prospective (cross-sectional)
United States
BAC chromosomal microarray V5 or 6; V6 of BCM oligonucleotide chromosomal microarray
AF 254, CVS 53
Advanced maternal age (33.5%), abnormal ultrasound finding (22.9%), family history of genetic disease (23.7%), abnormal fetal karyotype (7.6%), parental anxiety (9%), altered serum screening (2.5%), others (0.9%)
309
Maya et al15 (2010), retrospective (cross-sectional)
Israel
BAC using SignatureChip whole genome or oligonucleotide microarrays
AF 243, CVS 16
Advanced maternal age (22.7%), abnormal ultrasound finding (38%), familial congenital disease (16%), abnormal fetal karyotype (5.6%), parental anxiety (17%), altered serum screening (0.7%)
269
Fiorentino et al14 (2011), prospective (cross-sectional)
Italy
Whole-genome BAC microarrayseCytoChip Focus Constitutional
AF 938, CVS 99
Advanced maternal age 42.8%), altered serum screening (1.3%), abnormal ultrasound (4.6%), abnormal fetal karyotype (0.8%), family history of genetic disease (1.1%), parental anxiety (46.8%), others (2.4%)
1037
Wapner et al16 (2012), prospective (cross-sectional)
United States
Agilent 4-plex array and Affymetrix genomewide human SNP array 6.0
AF 1627, CVS 1910
Abnormal ultrasound finding (25.8%), advanced maternal age (47.9%), altered serum screening (19.3%), others (9.7%)
4282
Lee et al11 (2012), prospective (cross-sectional)
Taiwan
1-Mb resolution BAC from 2010, until 60-K oligonucleotide
AF 2926, CVS 82, fetal blood 93
Abnormal ultrasound findings (6.1%), altered serum screening (0.8%), advanced maternal age (60.2%), parental anxiety (31.1%)
3171
Armengol et al7 (2012), prospective
Spain
Not defined
AF 728, CVS 164, fetal blood 14
Abnormal ultrasound finding (19%), altered serum screening (25.9%), history of congenital disease (16%), advanced maternal age (30.1%), parental anxiety (6.6%), other (2.2%)
906
AF, amniotic fluid; AMA, advanced maternal age (35 years old); BAC, bacterial artificial chromosome; CVS, chorionic villus sampling; SNP, single nucleotide polymorphism. Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
PubMed, CENTRAL, Cochrane Register of Diagnostic Test Accuracy Studies, and EMBASE. The search strategy was specific for each database and included a combination of the medical subject headings and free-text terms for “comparative genomic hybridization” and “karyotype.” No language or publication status restrictions were imposed. We included articles from Jan. 1, 1980, through March 31, 2014. The full search strategies are listed in the Appendix. Other electronic sources were used to find additional studies, such as conference abstracts, Google Scholar, DARE, and PROSPERO. We looked for additional studies in the reference lists of selected articles and contacted authors about their
knowledge of published or unpublished articles. The results of searches were crosschecked to eliminate duplicates.
Eligibility criteria Studies We included cross-sectional, case-control, and cohort studies conducted from Jan. 1, 1980, through March 31, 2014. No language restrictions were imposed. Studies were required to report at least sensitivity and specificity or data to calculate these parameters. Participants Pregnant women who underwent chorionic villus sampling, amniocentesis, or cordocentesis to perform CGH and karyotyping.
There were no preferences with respect to any other demographic characteristics of the participants. Comparisons We intended to perform the following comparisons: Karyotype (reference standard) vs CGH (index test). Karyotype plus CGH vs karyotype. Karyotype plus CGH vs CGH. However, at the time of analysis, we determined that CGH diagnosed abnormalities that the karyotype did not. Therefore, we decided to create a reference standard according to the literature (karyotype þ CGH).
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ajog.org could not agree, a third reviewer (W.S.) made the final decision.
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FIGURE 2
Risk of bias within studies
Data collection process Relevant data were collected using a standardized data extraction sheet, which contained the following: study design, methods, participants, index test, standard of reference, and final outcome details. Reviewers confirmed all data entries and checked the entries at least twice for completeness and accuracy. If some information was missing, we contacted the authors to obtain the complete data.
Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
Outcomes Outcomes were sensitivity, specificity, and likelihood ratios for numeric and structural chromosomal abnormalities.
Exclusions We excluded studies using karyotype or CGH independently, and those in which data were unavailable to obtain sensitivity and specificity.
Study selection Two investigators (H.A.G-P., J.A-P.) independently and blindly screened the titles and abstracts to determine the potential usefulness of the articles. Two assessors (H.A.G-P., J.A-P.) applied eligibility criteria to the full-text articles during the final selection. When discrepancies occurred, a final decision was reached by consensus. If the 2 assessors
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FIGURE 3
Risk of bias across studies
Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
Risk of bias in and across individual studies The risk of bias was assessed independently by at least 2 researchers (H.A.GP., J.A-P.) using the QUADAS2 tool, which evaluates items related to the patient selection, the index and reference tests, the flow and timing, and the concerns about their applicability. We solved disagreements by consensus. The risk of bias table (within and across studies) was edited using Review Manager Software version 5.2 (RevMan; Cochrane Collaboration, Oxford, England) to illustrate the judgments for each study. Summary measures Analyses were performed in RevMan 5.2, OpenMeta[Analyst] (http://www.cebm. brown.edu/open_meta), and Stata 10 (StataCorp, College Station, TX) as needed. The sensitivity, specificity, likelihood ratios, and diagnostic odds ratios were measured for comparisons with 95% confidence intervals (CIs). We performed fixed effects or random effect metaanalysis according to the heterogeneity or homogeneity among the studies. We also performed forest plots and summary receiver operating characteristic for comparisons. Heterogeneity between trials was assessed through the I2 statistic. A value 50% can represent heterogeneity according to Higgins and Green13 (2011). We also intended to analyze heterogeneity according to the following: reference standard, clinical spectrum, type of method used, and age of the patient.
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FIGURE 4
CGH vs gold standard (CGH D karyotype): sensitivity and specificity forest plot
CGH, comparative genomic hybridization. Saldarriaga. Karyotype vs genomic hybridization for prenatal diagnosis of chromosomal abnormalities. Am J Obstet Gynecol 2014.
Additional analyses We intended to perform the following subgroup analysis: low- and high-risk pregnancies, history of chromosomal abnormalities, parents with chromosomal abnormalities, maternal age >37 years, biochemical screening plus maternal ultrasonography, and abnormalities detected on ultrasonography. However, the studies lacked sufficient data to perform these types of analyses. Sensitivity analysis We undertook a sensitivity analysis based on unknown significance variables considered important for analysis and results. Publication bias Publication bias was not assessed due to the number of studies found (1000 cases and review of the literature. Prenat Diagn 2012;32:351-61. 10. Shaffer LG, Dabell MP, Fisher AJ, et al. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn 2012;32: 976-85. 11. Lee C-N, Lin S-Y, Lin C-H, Shih J-C, Lin TH, Su Y-N. Clinical utility of array comparative genomic hybridization for prenatal diagnosis: a cohort study of 3171 pregnancies; editorial comment. BJOG 2012;119:614-25.
12. Hillman SC, Pretlove S, Coomarasamy A, et al. Additional information from array comparative genomic hybridization technology over conventional karyotyping in prenatal diagnosis: a systematic review and meta-analysis. Ultrasound Obstet Gynecol 2011;37:6-14. 13. Higgins J, Green S. Cochrane Handbook for Systematic Reviews of Interventions version 5.1. 0. The Cochrane Collaboration; 2011. Available at: www.cochrane-handbook.org. Accessed Jan. 15, 2014. 14. Fiorentino F, Caiazzo F, Napolitano S, et al. Introducing array comparative genomic hybridization into routine prenatal diagnosis practice: a prospective study on over 1000 consecutive clinical cases. Prenat Diagn 2011;31:1270-82. 15. Maya I, Davidov B, Gershovitz L, et al. Diagnostic utility of array-based comparative genomic hybridization (aCGH) in a prenatal setting. Prenat Diagn 2010;30:1131-7. 16. Wapner RJ, Martin CL, Levy B, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012;367: 2175-84. 17. Van den Veyver IB, Patel A, Shaw CA, et al. Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases. Prenat Diagn 2009;29:29-39. 18. American College of Obstetricians and Gynecologists. Array comparative genomic hybridization in prenatal diagnosis. ACOG Committee opinion no. 446. Obstet Gynecol 2009;114:1161-3. 19. Mansfield ES. Diagnosis of Down syndrome and other aneuploidies using quantitative polymerase chain reaction and small tandem repeat polymorphisms. Hum Mol Genet 1993;2:43-50. 20. Pertl B, Kopp S, Kroisel P, Tului L, Brambati B, Adinolfi M. Rapid detection of chromosome aneuploidies by quantitative fluorescence PCR: first application on 247 chorionic villus samples. J Med Genet 1999;36:300-3. 21. Schouten JP. Relative quantification of 40 nucleic acid sequences by multiplex ligationdependent probe amplification. Nucleic Acids Res 2002;30:e57. 22. Beaudet AL. Ethical issues raised by common copy number variants and single nucleotide polymorphisms of certain and uncertain significance in general medical practice. Genome Med 2010;2:42. 23. Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 2007;39(Suppl):S48-54. 24. Riggs ER, Church DM, Hanson K, et al. Towards an evidence-based process for the clinical interpretation of copy number variation. Clin Genet 2012;81:403-12. 25. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet 2004;36:949-51. 26. Giardino D, Corti C, Ballarati L, et al. De novo balanced chromosome rearrangements in prenatal diagnosis. Prenat Diagn 2009;29: 257-65.
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27. De Gregori M, Ciccone R, Magini P, et al. Cryptic deletions are a common finding in “balanced” reciprocal and complex chromosome rearrangements: a study of 59 patients. J Med Genet 2007;44:750-62. 28. Schluth-Bolard C, Delobel B, Sanlaville D, et al. Cryptic genomic imbalances in de novo and inherited apparently balanced chromosomal rearrangements: array CGH study of 47 unrelated cases. Eur J Med Genet 2009;52: 291-6. 29. Brady PD, Vermeesch JR. Genomic microarrays: a technology overview. Prenat Diagn 2012;32:336-43.
A PPENDIX Search strategies Search strategy for MEDLINE via PubMed: (‘Comparative genomic hybridization’ [mh] OR ‘a-CGH’ [tw] OR aCGH [tw] OR CGH [tw]) AND (Karyotype [mh] OR caryotype [tw] OR ‘chromosomal arrangement’ [tw] OR ‘chromosomal configuration’ [tw] OR ‘chromosomal pattern’ [tw] OR ‘chromosome arrangement’ [tw] OR kariotype [tw] OR karotype [tw] OR karytype [tw]) AND (‘Prenatal diagnosis’ [mh] OR ‘Fetal aneuploidy’ [mh] OR ‘Maternal serum screening’ [mh] OR ‘Chromosomal anomalies’ [tw] OR ‘Chromosomal defects’ [tw]) AND (‘Diagnostic test, routine’ [mh] OR ‘Sensitivity and specificity’ [mh] OR ‘Roc curve’ [mh] OR ‘Predictive value of tests’ [mh] OR Sensitivity [tw] OR Specificity [tw] OR Accuracy [tw] OR ‘Predictive value’ [tw] OR Likelihood [tw]) Search strategy for EMBASE: (comparative genomic hybridization [Emtree] OR ‘a-CGH’ [tw] OR aCGH [tw] OR CGH [tw]) AND (Karyotype [Emtree] OR caryotype [tw] OR ‘chromosomal arrangement’ [tw] OR ‘chromosomal configuration’ [tw] OR ‘chromosomal pattern’ [tw] OR ‘chromosome arrangement’ [tw] OR kariotype [tw] OR karotype [tw] OR karytype [tw]) AND (Prenatal diagnosis [Emtree] OR aneuploidy [Emtree] OR maternal serum screening test [Emtree] OR chromosome aberration [Emtree]) AND (Diagnostic accuracy [Emtree] OR Sensitivity and specificity [Emtree] OR receiver operating characteristic
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[Emtree] OR Predictive value [Emtree] OR Likelihood [tw]) Search strategy for CENTRAL and Cochrane Register of Diagnostic Test Accuracy Studies: (‘Comparative genomic hybridization’ [mh] OR ‘a-CGH’ [tw] OR aCGH [tw] OR CGH [tw]) AND (Karyotype [mh] OR
ajog.org caryotype [tw] OR ‘chromosomal arrangement’ [tw] OR ‘chromosomal configuration’ [tw] OR ‘chromosomal pattern’ [tw] OR ‘chromosome arrangement’ [tw] OR kariotype [tw] OR karotype [tw] OR karytype [tw]) AND (‘Prenatal diagnosis’ [mh] OR ‘Fetal aneuploidy’ [mh] OR ‘Maternal serum screening’
[mh] OR ‘Chromosomal anomalies’ [tw] OR ‘Chromosomal defects’ [tw]) AND (‘Diagnostic test, routine’ [mh] OR ‘Sensitivity and specificity’ [mh] OR ‘Roc curve’ [mh] OR ‘Predictive value of tests’ [mh] OR Sensitivity [tw] OR Specificity [tw] OR Accuracy [tw] OR ‘Predictive value’ [tw] OR Likelihood [tw])
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