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."
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Search term: Comparative Genomic Hybridization'

<pubmed limit=5>Comparative Genomic Hybridization</pubmed>

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. <pubmed>27382234</pubmed>
  2. <pubmed>22551147</pubmed>
  3. <pubmed>20576126</pubmed>| BMC Med Genet.
  4. <pubmed>20168112</pubmed>
  5. <pubmed>19546809</pubmed>
  6. <pubmed>20538352</pubmed>
  7. <pubmed>19624846</pubmed> | BMC
  8. <pubmed>16968546</pubmed>| BMC Cancer

Reviews

<pubmed>20494259</pubmed>


Articles

<pubmed>19795450</pubmed> <pubmed>15127362</pubmed>

Search PubMed

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



Prenatal Diagnosis Terms

  • 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.
  • free β human chorionic gonadotrophin - beta-hCG subunit of hCG used as a diagnostic marker for: early detection of pregnancy, Trisomy 21, spontaneous abortion, ectopic pregnancy, hydatidiform mole or choriocarcinoma.
  • multiples of the median - (MoM) A multiple of the median is a measure of how far an individual test result deviates from the median and is used to report the results of medical screening tests, particularly where the results of the individual tests are highly variable.
  • 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. (2018, December 18) Embryology Comparative Genomic Hybridization. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Comparative_Genomic_Hybridization

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© Dr Mark Hill 2018, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G