Comparative Genomic Hybridization

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Introduction

Detection of chromosomal aberrations

This new test under development is based upon microarray-based comparative genomic hybridization (array CGH). All fetal cells should have complete copies of maternal and paternal genomes. The test compares regions of fetal DNA that deviate from this "pattern" due to either too much or too little DNA, alterations reflect regions of the genome that are either copied or deleted. These genetic changes may therefore cause disease.


Any two unrelated people have the same 99.9% DNA sequences, the remaining 0.1% is the genetic variants that influence how people differ in their risk of disease or their response to drugs.


Diagnosis Links: Prenatal Diagnosis | Pregnancy Test | Amniocentesis | Chorionic villus sampling | Ultrasound | Alpha-Fetoprotein | Pregnancy-associated plasma protein-A | Fetal Blood Sampling | Magnetic Resonance Imaging | Computed Tomography | Non-Invasive Prenatal Testing | Fetal Cells in Maternal Blood | Preimplantation Genetic Screening | Comparative Genomic Hybridization | Genome Sequencing | Neonatal Diagnosis | Category:Prenatal Diagnosis | Fetal Surgery | Classification of Diseases | Category:Neonatal Diagnosis

Some Recent Findings

  • Preimplantation genetic screening for all 24 chromosomes by microarray comparative genomic hybridization significantly increases implantation rates and clinical pregnancy rates in patients undergoing in vitro fertilization with poor prognosis[1] "A majority of human embryos produced in vitro are aneuploid, especially in couples undergoing in vitro fertilization (IVF) with poor prognosis. Preimplantation genetic screening (PGS) for all 24 chromosomes has the potential to select the most euploid embryos for transfer in such cases. ... In this pilot study, we have shown that PGS by array CGH can improve the clinical outcome in patients undergoing IVF with poor prognosis."
  • A noninvasive test to determine paternity in pregnancy[2] "Our approach shows that noninvasive prenatal paternity testing can be performed within the first trimester with the use of a maternal blood sample." Non-Invasive Prenatal Testing
  • Application of a target array comparative genomic hybridization to prenatal diagnosis[3]"In the 132 reference materials, all known genomic alterations were successfully identified. In the 94 clinical samples that were also subjected to conventional karyotyping, three cases of balanced chromosomal aberrations were not detected by aCGH. However, we identified eight cases of microdeletions in the Yq11.23 chromosomal region that were not found by conventional karyotyping. This region harbors the DAZ gene, and deletions may lead to non-obstructive spermatogenesis."
  • Array comparative genomic hybridization for genetic evaluation of fetal loss between 10 and 20 weeks of gestation [4] "Array comparative genomic hybridization detected de novo copy number changes in 13% of cases where routine cytogenetic testing was normal or not performed. These involved large regions of DNA and may provide novel explanations for some cases of otherwise unexplained pregnancy loss."
  • Molecular diagnosis of mitochondrial DNA deletion and depletion syndromes.[5] "We conclude that this custom array is capable of reliably detecting mitochondrial DNA deletion with elucidation of the deletion break points and the percentage of heteroplasmy. In addition, simultaneous detection of the copy number changes in both nuclear and mitochondrial genomes makes this dual genome array of tremendous value in the diagnoses of mitochondrial DNA depletion syndromes."
  • Newborn hearing screening and genetic testing in 8974 Brazilian neonates.[6]"We have found 17 individuals who failed in transient otoacoustic emissions (TOAE). Among them, we detected 4 homozygous newborns for 35delG mutation and 3 individuals with A827G mutation in the MTRNR1 mitochondrial gene."
  • Whole genome microarray analysis, from neonatal blood cards. [7]] "Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology. ...Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing."
More recent papers  
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Search term: Comparative Genomic Hybridization'

Alexandra Galvão Gomes, Carlos H Paiva Grangeiro, Luiz R Silva, Flávia G Oliveira-Gennaro, Ciro S Pereira, Tatiana M Joaquim, Rodrigo A Panepucci, Jeremy A Squire, Lucia Martelli Complex Mosaic Ring Chromosome 11 Associated with Hemizygous Loss of 8.6 Mb of 11q24.2qter in Atypical Jacobsen Syndrome. Mol Syndromol: 2017, 8(1);45-49 PubMed 28232783

Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla Functionally-focused algorithmic analysis of high resolution microarray-CGH genomic landscapes demonstrates comparable genomic copy number aberrations in MSI and MSS sporadic colorectal cancer. PLoS ONE: 2017, 12(2);e0171690 PubMed 28231327

Fiona Blanco-Kelly, María Palomares, Elena Vallespín, Cristina Villaverde, Rubén Martín-Arenas, Camilo Vélez-Monsalve, Isabel Lorda-Sánchez, Julián Nevado, María José Trujillo-Tiebas, Pablo Lapunzina, Carmen Ayuso, Marta Corton Improving molecular diagnosis of aniridia and WAGR syndrome using customized targeted array-based CGH. PLoS ONE: 2017, 12(2);e0172363 PubMed 28231309

Hong-Dan Wang, Lin Liu, Dong Wu, Tao Li, Cun-Ying Cui, Lian-Zhong Zhang, Cheng-Zeng Wang Clinical and molecular cytogenetic analyses of four families with 1q21.1 microdeletion or microduplication. J Gene Med: 2017; PubMed 28220983

Aditi Kotdawala, Deven Patel, Javier Herrero, Rajni Khajuria, Nalini Mahajan, Manish Banker Aneuploidy screening by array comparative genomic hybridization improves success rates of in vitro fertilization: A multicenter Indian study. J Hum Reprod Sci: 2017, 9(4);223-229 PubMed 28216909

Microarray

Ideogram showing genetic imbalances detected in 71 medulloblastoma[8]

Microarrays are a new technique that allows a large number of different genetic sequences to be arrayed on a slide which can then be used to identify specific sequences in an unknown mix of either DNA or RNA. This technique required the development of DNA synthetic techniques and microprocessor controlled robotics for array design and has been used extensively in cell biology.

What is an array? "to place in an orderly arrangement" Think of a hairbrush with each "hair" dipped in individual coloured inks and applied to paper. Each "hair" would makes an individual coloured "spot". Now consider instead of ink, if each hair had a different piece of DNA then a specific pattern is generated.

Microarray technology.jpg

References

  1. Gaurav Majumdar, Abha Majumdar, Meena Lall, Ishwar C Verma, Kailash C Upadhyaya Preimplantation genetic screening for all 24 chromosomes by microarray comparative genomic hybridization significantly increases implantation rates and clinical pregnancy rates in patients undergoing in vitro fertilization with poor prognosis. J Hum Reprod Sci: 2016, 9(2);94-100 PubMed 27382234
  2. Xin Guo, Philip Bayliss, Marian Damewood, John Varney, Emily Ma, Brett Vallecillo, Ravinder Dhallan A noninvasive test to determine paternity in pregnancy. N. Engl. J. Med.: 2012, 366(18);1743-5 PubMed 22551147
  3. Ji Hyeon Park, Jung Hoon Woo, Sung Han Shim, Song-Ju Yang, Young Min Choi, Kap-Seok Yang, Dong Hyun Cha Application of a target array comparative genomic hybridization to prenatal diagnosis. BMC Med. Genet.: 2010, 11;102 PubMed 20576126 | BMC Med Genet.
  4. Jennifer E Warren, David K Turok, Teresa M Maxwell, Arthur R Brothman, Robert M Silver Array comparative genomic hybridization for genetic evaluation of fetal loss between 10 and 20 weeks of gestation. Obstet Gynecol: 2009, 114(5);1093-102 PubMed 20168112
  5. A Craig Chinault, Chad A Shaw, Ellen K Brundage, Lin-Ya Tang, Lee-Jun C Wong Application of dual-genome oligonucleotide array-based comparative genomic hybridization to the molecular diagnosis of mitochondrial DNA deletion and depletion syndromes. Genet. Med.: 2009, 11(7);518-26 PubMed 19546809
  6. Karin de A B Nivoloni, Sueli M da Silva-Costa, Mariza C A Pomílio, Tânia Pereira, Karen de C Lopes, Vanessa C S de Moraes, Fabiana Alexandrino, Camila A de Oliveira, Edi L Sartorato Newborn hearing screening and genetic testing in 8974 Brazilian neonates. Int. J. Pediatr. Otorhinolaryngol.: 2010, 74(8);926-9 PubMed 20538352
  7. Jill Hardin, Richard H Finnell, David Wong, Michael E Hogan, Joy Horovitz, Jenny Shu, Gary M Shaw Whole genome microarray analysis, from neonatal blood cards. BMC Genet.: 2009, 10;38 PubMed 19624846 | BMC
  8. Massimiliano De Bortoli, Robert C Castellino, Xin-Yan Lu, Jeffrey Deyo, Lisa Marie Sturla, Adekunle M Adesina, Laszlo Perlaky, Scott L Pomeroy, Ching C Lau, Tsz-Kwong Man, Pulivarthi H Rao, John Y H Kim Medulloblastoma outcome is adversely associated with overexpression of EEF1D, RPL30, and RPS20 on the long arm of chromosome 8. BMC Cancer: 2006, 6;223 PubMed 16968546 | BMC Cancer

Reviews

Gary Fruhman, Ignatia B Van den Veyver Applications of array comparative genomic hybridization in obstetrics. Obstet. Gynecol. Clin. North Am.: 2010, 37(1);71-85, Table of Contents PubMed 20494259


Articles

Justine Coppinger, Sarah Alliman, Allen N Lamb, Beth S Torchia, Bassem A Bejjani, Lisa G Shaffer Whole-genome microarray analysis in prenatal specimens identifies clinically significant chromosome alterations without increase in results of unclear significance compared to targeted microarray. Prenat. Diagn.: 2009, 29(12);1156-66 PubMed 19795450

Anthony J Schaeffer, June Chung, Konstantina Heretis, Andrew Wong, David H Ledbetter, Christa Lese Martin Comparative genomic hybridization-array analysis enhances the detection of aneuploidies and submicroscopic imbalances in spontaneous miscarriages. Am. J. Hum. Genet.: 2004, 74(6);1168-74 PubMed 15127362


Search PubMed

Search PubMed: Prenatal Diagnosis Comparative Genomic Hybridization | Comparative Genomic Hybridization



Prenatal Diagnosis Terms

  • ART - Assisted Reproductive Technology a general term to describe all the clinical techniques used to aid fertility.
  • blastomere biopsy - An ART preimplantation genetic diagnosis technique carried out at cleavage stage (day 3), excluding poor quality embryos, detects chromosomal abnormalities of both maternal and paternal origin. May not detect cellular mosaicism in the embryo.
  • blastocyst biopsy - An ART preimplantation genetic diagnosis technique carried out at blastocyst stage (day 4-5), removes several trophoblast (trophoderm) cells, detects chromosomal abnormalities of both maternal and paternal origin and may detect cellular mosaicism.
  • cell-free fetal deoxyribonucleic acid - (cffDNA) refers to fetal DNA circulating and isolated from the plasma portion of maternal blood.
  • false negative rate - The proportion of pregnancies that will test negative given that the congenital anomaly is present.
  • false positive rate - The proportion of pregnancies that will test positive given that the congenital anomaly is absent.
  • negative predictive value - The probability that a congenital anomaly is absent given that the prenatal screening test is negative.
  • Non-Invasive Prenatal Testing - (NIPT) could refer to ultrasound or other imaging techniques, but more frequently used to describe analysis of cell-free fetal DNA circulating in maternal blood.
  • polar body biopsy - (PB biopsy) An ART preimplantation genetic diagnosis technique that removes either the first or second polar body from the zygote. As these are generated by oocyte meiosis they detects chromosomal abnormalities only on the female genetics.
  • positive predictive value - The probability that a congenital anomaly is present given that the prenatal screening test is positive.
  • pre-implantation genetic diagnosis - (PGD, pre-implantation genetic screening) a diagnostic procedure for embryos produced through Assisted Reproductive Technology (ART, in vitro fertilisation, IVF) for genetic diseases that would generate developmental abnormalities or serious postnatal diseases.
  • prenatal screening sensitivity - (detection rate) The probability of testing positive on a prenatal screening test if the congenital anomaly is present.
  • prenatal screening specificity - The probability of testing negative on a prenatal screening test if the congenital anomaly is absent.
  • single nucleotide polymorphisms - (SNPs) the variation in a single DNA nucleotide that occurs at a specific position in the genome.
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Cite this page: Hill, M.A. 2017 Embryology Comparative Genomic Hybridization. Retrieved February 27, 2017, from https://embryology.med.unsw.edu.au/embryology/index.php/Comparative_Genomic_Hybridization

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