Araştırma Makalesi
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Diagnostic Outcomes for Genetic Testing of 54 Genes in Pregnancy Loss Using Array CGH Method: A Two-Year Retrospective Study

Yıl 2020, Cilt: 17 Sayı: 4, 599 - 609, 31.12.2020
https://doi.org/10.38136/jgon.771393

Öz

Objective: The current study aimed to retrospectively evaluate different diag- nostic approaches for the array genetic analysis of the cases from all trimester fetal loss in the medical genetics clinic between 2016 and 2017. The Quantitati- ve Fluorescent Polymerase Chain Reaction(QFPCR) test was performed on 50 samples, and aneuploidy was detected in 11 samples as a result of the test, and the array-CGH was performed when 39 QF-PCR resulted in normal test results. Under this purpose, we aimed to analyze and determine the possible copy num- ber variation(CNV), gene deletions, and/or duplications involved in embryonic cell division, tissue differentiation, intended.
Materials and methods: DNA isolation from cases of this retrospective study was completed using the PureLink Genomic DNA isolation kit. DNA samples were then genoty - ped for molecular etiological reasons by oligonücleotid microarray -CGH method (aCGH , 60 K ISCA design , Agilent , Germany ). Hybridized probe correlations of the case and reference DNAs were evaluated with databases (Database of Genomic Variants Analysis ) used in genomic variation analysis in terms of 54 functional genes CNVs associated with intrauterine losses.
Results: CNV was detected in 30 (77%) of 39 fetal samples analyzed within the scope of the research. Fifty-five percent of CNVs were found to be duplication (55%) and forty-five percent were deletions (45%). As a result of the evaluation, deletion was detected in 19 (35%) of 54 genes, duplication was detected in 26 (48%), while in 3 (6%) both deletion and duplication were detected. Although CNV detected in autosomal chromosomes (chromosome 1, 2, 3, 4, 5, 7, 8, 10, 12, 13, 14, 15 and 20), CNV was established the most common in X chromosome. In our study, CNVs associated with COX7B, ZIC1, MECP2, FMR1, HOXD13, JAG1, MSX2, NEXN, and SIX3 genes were found to be more frequent in terms of fetal loss etiology.

Conclusions: Based on our experience, the array-CGH method can be used to investigate the etiology of the normal results of QF-PCR in cases of fetal loss. The array CGH method will be preferred more and more due to the ease of application and the data obtained. When we look at the literature, it is seen that there is not enough research on array CGH about fetal loss and more studies are needed to increase the experience in this field.

Proje Numarası

2017-E.66893

Kaynakça

  • 1. Smith GCS. Screening and prevention of stillbirth. Best Pract Res Clin Obstet Gynaecol. 2017;38:71–82.
  • 2. Sahoo T, Dzidic N, Strecker MN, Commander S, Travis MK, Doherty C, et al. Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges. Genet Med. 2017;19(1):83–9.
  • 3. Harris RA, Ferrari F, Ben‐Shachar S, Wang X, Saade G, Van Den Veyver I, et al. Genome‐wide array‐based copy number profiling in human placentas from unexplained stillbirths. Prenat Diagn. 2011;31(10):932–44.
  • 4. Donaghue C, Davies N, Ahn JW, Thomas H, Ogilvie CM, Mann K. Efficient and cost-effective genetic analysis of products of conception and fetal tissues using a QF-PCR/array CGH strategy; five years of data. Mol Cytogenet. 2017;10(1):12.
  • 5. Massalska D, Zimowski JG, Bijok J, Pawelec M, Czubak‐Barlik M, Jakiel G, et al. First trimester pregnancy loss: clinical implications of genetic testing. J Obstet Gynaecol Res. 2017;43(1):23–9.
  • 6. Raca G, Artzer A, Thorson L, Huber S, Modaff P, Laffin J, et al. Array‐based comparative genomic hybridization (aCGH) in the genetic evaluation of stillbirth. Am J Med Genet Part A. 2009;149(11):2437–43.
  • 7. Rosenfeld JA, Tucker ME, Escobar LF, Neill NJ, Torchia BS, McDaniel LD, et al. Diagnostic utility of microarray testing in pregnancy loss. Ultrasound Obstet Gynecol. 2015;46(4):478–86.
  • 8. Nijkamp JW, Sebire NJ, Bouman K, Korteweg FJ, Erwich J, Gordijn SJ. Perinatal death investigations: What is current practice? In: Seminars in Fetal and Neonatal Medicine. Elsevier; 2017. p. 167–75.
  • 9. Kaya ÖÖ, Koç A, Özdemir TR, Kirbiyik Ö, Özyilmaz B, Özeren M, et al. QF-PCR in invasive prenatal diagnosis: a single-center experience in Turkey. Turkish J Med Sci. 2017;47(1):142–7.
  • 10. Coughlin CR, Scharer GH, Shaikh TH. Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med. 2012;4(10):80.
  • 11. Wou K, Hyun Y, Chitayat D, Vlasschaert M, Chong K, Wasim S, et al. Analysis of tissue from products of conception and perinatal losses using QF-PCR and microarray: A three-year retrospective study resulting in an efficient protocol. Eur J Med Genet. 2016;59(8):417–24.
  • 12. Scott F, Murphy K, Carey L, Greville W, Mansfield N, Barahona P, et al. Prenatal diagnosis using combined quantitative fluorescent polymerase chain reaction and array comparative genomic hybridization analysis as a first‐line test: results from over 1000 consecutive cases. Ultrasound Obstet Gynecol. 2013;41(5):500–7.
  • 13. Ceylan CA. Array CGH’te saptanan kopya sayisi değişikliklerinin klinikle ve kantitatif pcr ile değerlendirilmesi. Hacettepe Üniversitesi; 2015.
  • 14. Menten B, Swerts K, Delle Chiaie B, Janssens S, Buysse K, Philippé J, et al. Array comparative genomic hybridization and flow cytometry analysis of spontaneous abortions and mors in utero samples. BMC Med Genet. 2009;10(1):89.
  • 15. Reddy UM, Page GP, Saade GR, Silver RM, Thorsten VR, Parker CB, et al. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med. 2012;367(23):2185–93.

Gebelik Kayıplarında 54 Genin Array CGH Metoduyla Yapılan Tanısal Sonuçları: İki Yıllık Retrospektif Çalışma

Yıl 2020, Cilt: 17 Sayı: 4, 599 - 609, 31.12.2020
https://doi.org/10.38136/jgon.771393

Öz

Amaç:

Bu çalışma, 2016 ve 2017 yılları arasında tıbbi genetik kliniğine gelen tüm gebelik trimesterlerinde, fetal kayıp olgularına farklı bir tanısal yaklaşım olarak uygulanmış olan array-CGH genetik analizinin retrospektif olarak değerlendirmesini incelemeyi amaçlamıştır. 50 örnek üzerinde Kantitatif Floresan Polimeraz Zincir Reaksiyonu (QF-PCR) testi yapıldı ve test sonucunda 11 örnekte anöploidi saptandı ve QF-PCR normal olan 39 örneğe array-CGH analizi gerçekleştirildi. Bu amaçla, embriyonik dönemde hücre bölünmesi, doku farklılaşması aşamalarında etkili delesyon ve duplikasyonları, olası kopya sayısı varyasyonlarını (CNV) analiz etmeyi ve belirlemeyi amaçladık.

Gereç ve Yöntemler:

Bu retrospektif çalışmada vakaların abortus ve fetal biopsi örneklerinden yapılan DNA izolasyonunda PureLink Genomik DNA izolasyon kiti kullanıldı. DNA numuneleri daha sonra oligonükleotid array-CGH yöntemi (aCGH, 60 K ISCA tasarımı, Agilent, Almanya) ile moleküler etiyolojik nedenler açısından incelendi. Olgu ve referans DNA'ların hibridize prob korelasyonları, intrauterin kayıplarla ilişkili 54 fonksiyonel gen CNV açısından genomik varyasyon analizinde kullanılan veri tabanları (Genomik Varyantlar Analizi Veritabanı) ile değerlendirildi.

Bulgular:

Araştırma kapsamında analiz edilen 39 fetal örneğin 30'unda (% 77) CNV saptandı. CNV'lerin yüzde elli beşi duplikasyon (% 55) ve yüzde kırk beşi delesyon (% 45) şeklinde bulundu. Değerlendirme sonucunda 54 genin 19'unda (% 35) delesyon, 26'sında (% 48) duplikasyon, 3'ünde (% 6) hem delesyon hem de duplikasyon saptandı. Otozomal kromozomlarda CNV tespit edilmesine rağmen (kromozom 1, 2, 3, 4, 5, 7, 8, 10, 12, 13, 14, 15 ve 20), en sık CNV X kromozomunda saptandı. Çalışmamızda COX7B, ZIC1, MECP2,

FMR1, HOXD13, JAG1, MSX2, NEXN ve SIX3 genleri ile ilişkili CNV'lerin fetal kayıp etiyolojisi açısından daha sık olduğu bulunmuştur.

Sonuç:

Deneyimlerimize dayanarak, array-CGH yöntemi, fetal kayıp vakalarında QF-PCR ile normal sonuçlanmış vakaların etiyolojisini araştırmak için kullanılabilir. Array-CGH yöntemi uygulama kolaylığı ve elde edilen veriler nedeniyle giderek daha fazla tercih edilecektir. Literatüre baktığımızda, array-CGH yöntemi üzerinde fetal kayıplar hakkında yeterli araştırma olmadığı ve bu alandaki deneyimi arttırmak için daha fazla çalışmaya ihtiyaç olduğu görülmektedir.

Proje Numarası

2017-E.66893

Kaynakça

  • 1. Smith GCS. Screening and prevention of stillbirth. Best Pract Res Clin Obstet Gynaecol. 2017;38:71–82.
  • 2. Sahoo T, Dzidic N, Strecker MN, Commander S, Travis MK, Doherty C, et al. Comprehensive genetic analysis of pregnancy loss by chromosomal microarrays: outcomes, benefits, and challenges. Genet Med. 2017;19(1):83–9.
  • 3. Harris RA, Ferrari F, Ben‐Shachar S, Wang X, Saade G, Van Den Veyver I, et al. Genome‐wide array‐based copy number profiling in human placentas from unexplained stillbirths. Prenat Diagn. 2011;31(10):932–44.
  • 4. Donaghue C, Davies N, Ahn JW, Thomas H, Ogilvie CM, Mann K. Efficient and cost-effective genetic analysis of products of conception and fetal tissues using a QF-PCR/array CGH strategy; five years of data. Mol Cytogenet. 2017;10(1):12.
  • 5. Massalska D, Zimowski JG, Bijok J, Pawelec M, Czubak‐Barlik M, Jakiel G, et al. First trimester pregnancy loss: clinical implications of genetic testing. J Obstet Gynaecol Res. 2017;43(1):23–9.
  • 6. Raca G, Artzer A, Thorson L, Huber S, Modaff P, Laffin J, et al. Array‐based comparative genomic hybridization (aCGH) in the genetic evaluation of stillbirth. Am J Med Genet Part A. 2009;149(11):2437–43.
  • 7. Rosenfeld JA, Tucker ME, Escobar LF, Neill NJ, Torchia BS, McDaniel LD, et al. Diagnostic utility of microarray testing in pregnancy loss. Ultrasound Obstet Gynecol. 2015;46(4):478–86.
  • 8. Nijkamp JW, Sebire NJ, Bouman K, Korteweg FJ, Erwich J, Gordijn SJ. Perinatal death investigations: What is current practice? In: Seminars in Fetal and Neonatal Medicine. Elsevier; 2017. p. 167–75.
  • 9. Kaya ÖÖ, Koç A, Özdemir TR, Kirbiyik Ö, Özyilmaz B, Özeren M, et al. QF-PCR in invasive prenatal diagnosis: a single-center experience in Turkey. Turkish J Med Sci. 2017;47(1):142–7.
  • 10. Coughlin CR, Scharer GH, Shaikh TH. Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med. 2012;4(10):80.
  • 11. Wou K, Hyun Y, Chitayat D, Vlasschaert M, Chong K, Wasim S, et al. Analysis of tissue from products of conception and perinatal losses using QF-PCR and microarray: A three-year retrospective study resulting in an efficient protocol. Eur J Med Genet. 2016;59(8):417–24.
  • 12. Scott F, Murphy K, Carey L, Greville W, Mansfield N, Barahona P, et al. Prenatal diagnosis using combined quantitative fluorescent polymerase chain reaction and array comparative genomic hybridization analysis as a first‐line test: results from over 1000 consecutive cases. Ultrasound Obstet Gynecol. 2013;41(5):500–7.
  • 13. Ceylan CA. Array CGH’te saptanan kopya sayisi değişikliklerinin klinikle ve kantitatif pcr ile değerlendirilmesi. Hacettepe Üniversitesi; 2015.
  • 14. Menten B, Swerts K, Delle Chiaie B, Janssens S, Buysse K, Philippé J, et al. Array comparative genomic hybridization and flow cytometry analysis of spontaneous abortions and mors in utero samples. BMC Med Genet. 2009;10(1):89.
  • 15. Reddy UM, Page GP, Saade GR, Silver RM, Thorsten VR, Parker CB, et al. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med. 2012;367(23):2185–93.
Toplam 15 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Sağlık Kurumları Yönetimi
Bölüm Araştırma Makaleleri
Yazarlar

Barış Paksoy 0000-0002-5101-2939

Ozturk Ozdemır 0000-0003-1057-3235

Fatma Sılan 0000-0001-7191-2240

Proje Numarası 2017-E.66893
Yayımlanma Tarihi 31 Aralık 2020
Gönderilme Tarihi 20 Temmuz 2020
Kabul Tarihi 16 Eylül 2020
Yayımlandığı Sayı Yıl 2020 Cilt: 17 Sayı: 4

Kaynak Göster

Vancouver Paksoy B, Ozdemır O, Sılan F. Diagnostic Outcomes for Genetic Testing of 54 Genes in Pregnancy Loss Using Array CGH Method: A Two-Year Retrospective Study. JGON. 2020;17(4):599-60.