المؤلفون: Corsten-Janssen, N, Bouman, K, Diphoorn, J C D, Scheper, A J, Kinds, R, El Mecky, J, Breet, H, Verheij, J B G M, Suijkerbuijk, R, Duin, L K, Manten, G T R, van Langen, I M, Sijmons, R H, Sikkema-Raddatz, B, Westers, H, van Diemen, C C

المصدر: Corsten-Janssen , N , Bouman , K , Diphoorn , J C D , Scheper , A J , Kinds , R , El Mecky , J , Breet , H , Verheij , J B G M , Suijkerbuijk , R , Duin , L K , Manten , G T R , van Langen , I M , Sijmons , R H , Sikkema-Raddatz , B , Westers , H & van Diemen , C C 2020 , ' A prospective study on rapid exome sequencing as a diagnostic test for multiple congenital anomalies on fetal ultrasound ....

الوصف: Objective: Conventional genetic tests (quantitative fluorescent-PCR [QF-PCR] and single nucleotide polymorphism-array) only diagnose ~40% of fetuses showing ultrasound abnormalities. Rapid exome sequencing (rES) may improve this diagnostic yield, but includes challenges such as uncertainties in fetal phenotyping, variant interpretation, incidental unsolicited findings, and rapid turnaround times. In this study, we implemented rES in prenatal care to increase diagnostic yield. Methods: We prospectively studied 55 fetuses. Inclusion criteria were: (a) two or more independent major fetal anomalies, (b) hydrops fetalis or bilateral renal cysts alone, or (c) one major fetal anomaly and a first-degree relative with the same anomaly. In addition to conventional genetic tests, we performed trio rES analysis using a custom virtual gene panel of ~3850 Online Mendelian Inheritance in Man (OMIM) genes. Results: We established a genetic rES-based diagnosis in 8 out of 23 fetuses (35%) without QF-PCR or array abnormalities. Diagnoses included MIRAGE (SAMD9), Zellweger (PEX1), Walker-Warburg (POMGNT1), Noonan (PTNP11), Kabuki (KMT2D), and CHARGE (CHD7) syndrome and two cases of Osteogenesis Imperfecta type 2 (COL1A1). In six cases, rES diagnosis aided perinatal management. The median turnaround time was 14 (range 8-20) days. Conclusion: Implementing rES as a routine test in the prenatal setting is challenging but technically feasible, with a promising diagnostic yield and significant clinical relevance.

وصف الملف: application/pdf

العلاقة: https://research.rug.nl/en/publications/87334dbf-bc3b-4511-963a-66c5ae7aad5cTest

الإتاحة: https://doi.org/10.1002/pd.5781Test
https://hdl.handle.net/11370/87334dbf-bc3b-4511-963a-66c5ae7aad5cTest
https://research.rug.nl/en/publications/87334dbf-bc3b-4511-963a-66c5ae7aad5cTest
https://pure.rug.nl/ws/files/151472886/A_prospective_study_on_rapid_exome_sequencing_as_a_diagnostic_test_for_multiple_congenital_anomalies_on_fetal_ultrasound.pdfTest

المؤلفون: Johansson, L. F., de Boer, E. N., de Weerd, H. A., van Dijk, F., Elferink, M. G., Schuring-Blom, G. H., Suijkerbuijk, R. F., Sinke, R. J., te Meerman, G. J., Sijmons, R. H., Swertz, M. A., Sikkema-Raddatz, B.

المصدر: Johansson , L F , de Boer , E N , de Weerd , H A , van Dijk , F , Elferink , M G , Schuring-Blom , G H , Suijkerbuijk , R F , Sinke , R J , te Meerman , G J , Sijmons , R H , Swertz , M A & Sikkema-Raddatz , B 2017 , ' Novel Algorithms for Improved Sensitivity in Non-Invasive Prenatal Testing ' , Scientific Reports , vol. 7 , no. 1 , 1838 . https://doi.org/10.1038/s41598-017-02031-5Test

مصطلحات موضوعية: CELL-FREE DNA, MATERNAL PLASMA, FETAL DNA, ANEUPLOIDY, DIAGNOSIS, BLOOD, AMPLIFICATION, TRISOMY-18, ALIGNMENT, BIAS

الوصف: Non-invasive prenatal testing (NIPT) of cell-free DNA in maternal plasma, which is a mixture of maternal DNA and a low percentage of fetal DNA, can detect fetal aneuploidies using massively parallel sequencing. Because of the low percentage of fetal DNA, methods with high sensitivity and precision are required. However, sequencing variation lowers sensitivity and hampers detection of trisomy samples. Therefore, we have developed three algorithms to improve sensitivity and specificity: the chi-squared-based variation reduction (chi(VR)-V-2), the regression-based Z-score (RBZ) and the Match QC score. The chi(VR)-V-2 reduces variability in sequence read counts per chromosome between samples, the RBZ allows for more precise trisomy prediction, and the Match QC score shows if the control group used is representative for a specific sample. We compared the performance of chi(VR)-V-2 to that of existing variation reduction algorithms (peak and GC correction) and that of RBZ to trisomy prediction algorithms (standard Z-score, normalized chromosome value and median-absolute-deviation-based Z-score). chi(VR)-V-2 and the RBZ both reduce variability more than existing methods, and thereby increase the sensitivity of the NIPT analysis. We found the optimal combination of algorithms was to use both GC correction and chi(VR)-V-2 for pre-processing and to use RBZ as the trisomy prediction method.

وصف الملف: application/pdf

العلاقة: https://research.rug.nl/en/publications/5f20f8ef-1a74-486c-a3a0-4c975d661c46Test

الإتاحة: https://doi.org/10.1038/s41598-017-02031-5Test
https://hdl.handle.net/11370/5f20f8ef-1a74-486c-a3a0-4c975d661c46Test
https://research.rug.nl/en/publications/5f20f8ef-1a74-486c-a3a0-4c975d661c46Test
https://pure.rug.nl/ws/files/47381845/Novel_Algorithms_for_Improved_Sensitivity_in_Non_Invasive_Prenatal_Testing.pdfTest

المؤلفون: Oepkes, D., Page-Christiaens, G.C.L. (G. C. Lieve), Bax, C.J. (Caroline), Bekker, M.N. (Mireille), Bilardo, C.M. (Caterina Maddalena), Boon, E.M.J. (Elles ), Schuring-Blom, G.H. (Heleen), Coumans, A. (Audrey), Faas, B.H.W. (Brigitte), Galjaard, R-J.H. (Robert-Jan), Go, A.T.J.I. (Attie), Henneman, L. (Lidewij), Macville, M.V.E. (Merryn), Pajkrt, E. (Eva), Suijkerbuijk, R. (Ron), Huijsdens-van Amsterdam, K. (Karin), Van Opstal, A.R.M. (Diane), Verweij, E.J.J. (E. J. Joanne), Weiss, M.M. (Marjan M.), Sistermans, E.A. (Erik)

المصدر: Prenatal Diagnosis vol. 36 no. 12, pp. 1083-1090

الوصف: Objective: To evaluate the clinical impact of nationwide implementation of genome-wide non-invasive prenatal testing (NIPT) in pregnancies at increased risk for fetal trisomies 21, 18 and 13 (TRIDENT study). Method: Women with elevated risk based on first trimester combined testing (FCT ≥ 1:200) or medical history, not advanced maternal age alone, were offered NIPT as contingent screening test, performed by Dutch University Medical laboratories. We analyzed uptake, test performance, redraw/failure rate, turn-around time and pregnancy outcome. Results: Between 1 April and 1 September 2014, 1413/23 232 (6%) women received a high-risk FCT result. Of these, 1211 (85.7%) chose NIPT. One hundred seventy-nine women had NIPT based on medical history. In total, 1386/1390 (99.7%) women received a result, 6 (0.4%) after redraw. Mean turn-around time was 14 days. Follow-up was available in 1376 (99.0%) pregnancies. NIPT correctly predicted 37/38 (97.4%) trisomies 21, 18 or 13 (29/30, 4/4 and 4/4 respectively); 5/1376 (0.4%) cases proved to be false positives: trisomies 21 (n = 2), 18 (n = 1) and 13 (n = 2). Estimated reduction in invasive testing was 62%. Conclusion: Introduction of NIPT in the Dutch National healthcare-funded Prenatal Screening Program resulted in high uptake and a vast reduction of invasive testing. Our study supports offering NIPT to pregnant women at increased risk for fetal trisomy. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.

وصف الملف: application/pdf

العلاقة: http://repub.eur.nl/pub/94873Test; urn:hdl:1765/94873

الإتاحة: https://doi.org/10.1002/pd.4945Test
http://repub.eur.nl/pub/94873Test

المؤلفون: Corsten-Janssen, N., Bouman, K., Scheper, A. J., Meems-Veldhuis, M. T., Verheij, J. B. G. M., Suijkerbuijk, R., Duin, L. K., Manten, G. T. R., van Langen, I. M., Sikkema-Raddatz, B., Westers, H., van Diemen, C. C.

المساهمون: Health Psychology Research (HPR), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)

المصدر: European Journal of Human Genetics, 28(SUPPL 1), 169-170. Nature Publishing Group

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=narcis______::ebbdeab637978532d32ccc36ff348df8Test
https://research.rug.nl/en/publications/321846ab-a45f-4dcd-b179-df98d4506e07Test

المؤلفون: Van Echten-Arends, J., Coonen, E., Reuters, B., Suijkerbuijk, R. F., Dul, E. C., Land, J. A., van Ravenswaaij-Arts, C. M. A.

المصدر: Van Echten-Arends , J , Coonen , E , Reuters , B , Suijkerbuijk , R F , Dul , E C , Land , J A & van Ravenswaaij-Arts , C M A 2013 , ' Preimplantation genetic diagnosis for X;autosome translocations: lessons from a case of misdiagnosis ' , Human Reproduction , vol. 28 , no. 11 , pp. 3141-3145 . https://doi.org/10.1093/humrep/det362Test

مصطلحات موضوعية: PGD, misdiagnosis, reciprocal translocation, X-autosome translocation, segregation types

الوصف: Preimplantation genetic diagnosis (PGD) is offered to couples carrying a reciprocal translocation in an attempt to increase their chance of phenotypically normal offspring. For the selection of embryos that are balanced for the translocation chromosomes, it is critical to use a combination of DNA probes that can take account of all the segregation patterns of the particular translocation. The frequency of the different segregation types differs depending on the chromosomes involved, the location of the breakpoints and the number of chiasmata and the sex of the carrier. We report on a case of misdiagnosis after PGD-fluorescence in situ hybridization in a female translocation 46,X,t(X;5)(q13;p14) carrier. Transfer of two embryos diagnosed as balanced for the translocation chromosomes resulted in a singleton pregnancy that miscarried at 8 weeks' gestational age. The unbalanced karyotype of the fetus was consistent with 3:1 segregation resulting in tertiary trisomy for the derivative chromosome 5:47, XX,+der(5)t(X;5)(q13;p14) mat. Based on additional molecular cytogenetic studies of fetal tissue and the initially investigated blastomeres, we concluded that the misdiagnosis was most probably due to a technical error, i.e. a partial hybridization failure or co-localization of the Xq/Yq subtelomere probe signals. No evidence for a normal cell line (mosaicism) was found in the fetus, which could have explained the discrepancy. This case demonstrates the importance of using two diagnostic probes or testing 2 cells to detect translocation products with potentially viable imbalance. X; autosome translocations are a special case due to the added complication of X chromosome inactivation and particular caution is advised when designing a PGD strategy. TRIAL REGISTRATION NUMBER: not applicable.

الإتاحة: https://doi.org/10.1093/humrep/det362Test
https://cris.maastrichtuniversity.nl/en/publications/3b6c2262-6d0e-4f9b-aed7-5dc308b4c5bdTest

المؤلفون: Boormans, EMA, Birnie, Erwin, Wildschut, Hajo, Schuring-Blom, GH, Oepkes, D, van Oppen, AC, Nijhuis, JG, Macville, MVE, Kooper, AJA, Huijsdens, K, Hoffer, MVJ, Go, A, Creemers, J, Bhola, SL, Bilardo, KM, Suijkerbuijk, R, Bouman, K, Galjaard, Robert-Jan, Bonsel, Gouke, van Lith, JMM

المصدر: Boormans , EMA , Birnie , E , Wildschut , H , Schuring-Blom , GH , Oepkes , D , van Oppen , AC , Nijhuis , JG , Macville , MVE , Kooper , AJA , Huijsdens , K , Hoffer , MVJ , Go , A , Creemers , J , Bhola , SL , Bilardo , KM , Suijkerbuijk , R , Bouman , K , Galjaard , R-J , Bonsel , G & van Lith , JMM 2008 , ' Multiplex ligation-dependent probe amplification versus karyotyping in prenatal diagnosis: the M.A.K.E. study ' , BMC ....

وصف الملف: application/pdf

الإتاحة: https://doi.org/10.1186/1471-2393-8-18Test
https://pure.eur.nl/en/publications/82853b3a-5adb-4cad-ab31-311d7da7b05cTest
https://pure.eur.nl/ws/files/46785487/18492228.pdfTest
http://hdl.handle.net/1765/23131Test

المؤلفون: Weiss, M. M., Galjaard, R. H., Sistermans, E. A., Bax, C. J., Bekker, M. N., de Die-Smulders, C. E. M., Feenstra, I., Hoffer, M. J. V., den Hollander, N. S., Knapen, M. F. C. M., van Langen, I. M., Lichtenbelt, K. D., Lombardi, P. M., van Maarle, M. C., van der Meij, K. R. M., Pieters, M. J., Schuring-Blom, G. H., Sikkel, E., Stevens, S. J., Suijkerbuijk, R. F., van der Ven, A. J. E. M., Van Opstal, D., Henneman, L., Macville, M. V.

المصدر: Weiss , M M , Galjaard , R H , Sistermans , E A , Bax , C J , Bekker , M N , de Die-Smulders , C E M , Feenstra , I , Hoffer , M J V , den Hollander , N S , Knapen , M F C M , van Langen , I M , Lichtenbelt , K D , Lombardi , P M , van Maarle , M C , van der Meij , K R M , Pieters , M J , Schuring-Blom , G H , Sikkel , E , ....

العلاقة: https://research.vumc.nl/en/publications/896257aa-5289-4935-be6e-26f5fddee2d8Test

الإتاحة: https://research.vumc.nl/en/publications/896257aa-5289-4935-be6e-26f5fddee2d8Test

المؤلفون: Mostert, M.M.C. (M. M C), Van De Pol, F. (Francien), Weghuis, D.O. (D. Olde), Suijkerbuijk, R. (Ron), Geurts van Kessel, A.H.M. (Ad), Echten, J. (Jannie) van, Oosterhuis, J.W. (Wolter), Looijenga, L.H.J. (Leendert)

المصدر: Cancer Genetics and Cytogenetics vol. 89 no. 2, pp. 146-152

الوصف: Comparative genomic hybridization (CGH) was carried out on 15 primary testicular germ cell tumors (TGCT) of adolescents and adults and two metastatic residual tumors after chemotherapeutic treatment. The results were compared with karyotypic data obtained form the same tumor specimens after direct harvesting of metaphases or short-term in vitro culture. Both techniques revealed that the most consistent abnormality in primary TGCT is gain of 12p-sequences. Although in most cases over-representation of the complete short arm was observed, CGH revealed a specific amplification of 12p11.1-p12.1 region in two independent primary tumors. In addition, loss of (parts of) chromosome 13 (always involving q31-qter), and gain of (parts of) chromosome 7 (mostly involving q11), (parts of) chromosome 8, and the X chromosome were detected in more than 25% of the tumors by this latter technique. Loss of 6q15-q21 in both res

وصف الملف: application/pdf

العلاقة: http://repub.eur.nl/pub/56693Test; urn:hdl:1765/56693

الإتاحة: https://doi.org/10.1016/0165-4608Test(96)00043-X
http://repub.eur.nl/pub/56693Test

المؤلفون: Van Der Burgt, C J, Merkx, G F, Janssen, A H, Mulder, J C, Suijkerbuijk, R F, Smeets, D F

مصطلحات موضوعية: Research Article

الوصف: A balanced complex chromosome rearrangement (CCR) involving four chromosomes is very rare and may lead to different types of aneuploid germ cells. We report a liveborn child with multiple congenital anomalies and an apparently balanced translocation, t(11;12). High resolution chromosome analysis in the mother showed a CCR involving chromosomes 5, 11, 12, and 16. In situ hybridisation showed that this CCR was the result of a five break rearrangement, and that the derivative chromosome 12 consisted of parts of chromosomes 5, 11, and 12. From this it could be deduced that the karyotype of the child was not balanced, but resulted in partial trisomy for 5q and partial monosomy for 12p. The clinical findings in the child were compatible with partial trisomy for 5q.

وصف الملف: text/html

العلاقة: http://jmg.bmj.com/cgi/content/short/29/10/739Test; http://dx.doi.org/10.1136/jmg.29.10.739Test

الإتاحة: https://doi.org/10.1136/jmg.29.10.739Test
http://jmg.bmj.com/cgi/content/short/29/10/739Test

المؤلفون: van de Wetering, M, Oosterwegel, M, Holstege, F, Dooyes, D, Suijkerbuijk, R, Geurts van Kessel, A, Clevers, H

المصدر: Journal of Biological Chemistry ; volume 267, issue 12, page 8530-8536 ; ISSN 0021-9258

مصطلحات موضوعية: Cell Biology, Molecular Biology, Biochemistry

الإتاحة: https://doi.org/10.1016/s0021-9258Test(18)42476-3
https://api.elsevier.com/content/article/PII:S0021925818424763?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S0021925818424763?httpAccept=text/plainTest