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4. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature

Author

van Jaarsveld, Richard H., Reilly, Jack, Cornips, Marie-Claire, Hadders, Michael A., Agolini, Emanuele, Ahimaz, Priyanka, Anyane-Yeboa, Kwame, Bellanger, Severine Audebert, van Binsbergen, Ellen, van den Boogaard, Marie-Jose, Brischoux-Boucher, Elise, Caylor, Raymond C., Ciolfi, Andrea, van Essen, Ton A.J., Fontana, Paolo, Hopman, Saskia, Iascone, Maria, Javier, Margaret M., Kamsteeg, Erik-Jan, Kerkhof, Jennifer, Kido, Jun, Kim, Hyung-Goo, Kleefstra, Tjitske, Lonardo, Fortunato, Lai, Abbe, Lev, Dorit, Levy, Michael A., Lewis, M.E. Suzanne, Lichty, Angie, Mannens, Marcel M.A.M., Matsumoto, Naomichi, Maya, Idit, McConkey, Haley, Megarbane, Andre, Michaud, Vincent, Miele, Evelina, Niceta, Marcello, Novelli, Antonio, Onesimo, Roberta, Pfundt, Rolph, Popp, Bernt, Prijoles, Eloise, Relator, Raissa, Redon, Sylvia, Rots, Dmitrijs, Rouault, Karen, Saida, Ken, Schieving, Jolanda, Tartaglia, Marco, Tenconi, Romano, Uguen, Kevin, Verbeek, Nienke, Walsh, Christopher A., Yosovich, Keren, Yuskaitis, Christopher J., Zampino, Giuseppe, Sadikovic, Bekim, Alders, Mariëlle, and Oegema, Renske

Published
2023
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6. The Diagnostic Yield of Chromosomal Microarray Analysis in Third-Trimester Fetal Abnormalities.

Author

Elron, Eyal, Maya, Idit, Shefer-Averbuch, Noa, Kahana, Sarit, Matar, Reut, Klein, Kochav, Agmon-Fishman, Ifat, Gurevitch, Merav, Basel-Salmon, Lina, and Levy, Michal

Subjects
*OLIGONUCLEOTIDE arrays, *MATERNAL age, *THIRD trimester of pregnancy, *FETAL growth retardation, *PRENATAL diagnosis, *RETROSPECTIVE studies, *FETAL ultrasonic imaging, *DESCRIPTIVE statistics, *ANEUPLOIDY, *GENETIC polymorphisms, *POLYHYDRAMNIOS, *FETAL abnormalities, *MEDICAL records, *ACQUISITION of data, *GESTATIONAL age, *AMNIOCENTESIS, *GENETIC testing
Abstract

Objective This study aimed to determine the diagnostic yield of chromosomal microarray analysis (CMA) performed in cases of fetal abnormalities detected during the third trimester of pregnancy. Study Design A retrospective review of medical records was conducted for women who underwent amniocentesis at or beyond 28 weeks of gestation between January 2017 and February 2023. CMA results of pregnancies with abnormal sonographic findings not detected before 28 weeks were included. Results A total of 482 fetuses met the inclusion criteria. The average maternal age was 31.3 years, and the average gestational age at amniocentesis was 32.3 weeks. The overall diagnostic yield of CMA was 6.2% (30 clinically significant copy number variations [CNVs]). The yield was 16.4% in cases with two or more fetal malformations, while cases with a single anomaly revealed a diagnostic yield of 7.3%. Cases presenting isolated polyhydramnios or isolated fetal growth restriction had a lower yield of 9.3 and 5.4%, respectively. Of the 30 clinically significant cases, 19 (or 63.4%) exhibited recurrent CNVs. The remaining 11 cases (or 36.6%) presented unique CNVs. The theoretical yield of Noninvasive Prenatal Testing (NIPT) in our cohort is 2% for aneuploidy, which implies that it could potentially miss up to 70% of the significant findings that could be identified by CMA. In 80% of the fetuses (or 24 out of 30) with clinically significant CNVs, the structural abnormalities detected on fetal ultrasound examinations corresponded with the CMA results. Conclusion The 6.2% detection rate of significant CNVs in late-onset fetal anomalies confirms the value of CMA in third-trimester amniocentesis. The findings underscore the necessity of CMA for detecting CNVs potentially overlooked by NIPT and emphasize the importance of thorough genetic counseling. Key Points CMA yields 6.2% for third-trimester anomalies. NIPT may miss 70% of CMA findings. Ultrasound matched 80% of CMA results. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Regions of Homozygocity size patterns among diverse ethnic groups in Israel: Toward tailored diagnostic reporting thresholds.

Author

Maya, Idit, Levy, Michal, Matar, Reut, Kahana, Sarit, Agmon‐Fishman, Ifaat, Klein, Cochava, Gurevitch, Merav, Basel‐Salmon, Lina, and Sagi‐Dain, Lena

Abstract

Long contiguous stretches of homozygosity or regions of homozygosity (ROH) are frequently detected via microarray and sequencing technologies. However, consensus on the establishment of specific size cutoffs for reporting ROH remains elusive. This study aims to assess the Total ROH Percentages (TRPS) and size of ROH segments across different ethnic origins, exploring potential disparities and proposing tailored diagnostic thresholds. This retrospective study included 13,035 microarray analyses conducted between 2017 to 2023. ROH segments on autosomal chromosomes were retrieved, and samples lacking ROH segments were excluded. The cohort was categorized based on reported ethnic origins, and TRPS and ROH segment size were analyzed for each origin. Distinct TRPS values were noted among different ethnic groups, ranging from median 0.36% in Ethiopian Jewish cohort and up to 6.42% in the Bedouin population. Wide range of 99th percentiles of ROH segment size for various origins was noted, ranging from 10.6 to 51.5 Mb. A significant correlation between ROH segment sizes and TRPS was noted in each origin. Statistically significant differences in ROH segment sizes were noted between the Jewish and the Israeli Arab/Druze origins in TRPS from 1% to 9.99%, whereas extremities of low (0.11%–0.99%) and high (over 10%) TRPS yielded no significant differences. In conclusion, as fixed absolute size thresholds may overlook pathogenic segments in certain populations while generating excessive reports in others, tailored approaches to define ROH reporting thresholds can be considered to facilitate the accuracy and clinical relevance of genomic analyses. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Teaching clinicians practical genomic medicine: 7 years’ experience in a tertiary care center

Author

Michaelson-Cohen, Rachel, Salzer-Sheelo, Liat, Sukenik-Halevy, Rivka, Koifman, Arie, Fellner, Avi, Reches, Adi, Marom, Daphna, Behar, Doron M., Sofrin-Drucker, Efrat, Zaks-Hoffer, Gal, Weiss-Hubshmann, Monika, Oresntein, Naama, Kropach-Gilad, Nesia, Rhurman-Shahar, Noa, Averbuch, Noa Shefer, Magal, Nurit, Bazak, Lily, Josefberg, Sagi, Matar, Reut, Goldberg, Yael, Shohat, Mordechai, Basel-Salmon, Lina, and Maya, Idit

Published
2020
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19. Exploring the factors affecting classification and reporting of uncertain prenatal microarray findings, using a “virtual fetus” model‐a pilot study

Author

Michaelson‐Cohen, Rachel, primary, Salzer, Liat Sheelo, additional, Brabbing‐Goldstein, Dana, additional, Yaron, Yuval, additional, Reches, Adi, additional, Yonath, Hagith, additional, Regev, Miriam, additional, Shani, Hagit, additional, Altarescu, Gheona, additional, Segel, Reeval, additional, Sukenik‐Halevy, Rivka, additional, Daum, Hagit, additional, Harel, Tamar, additional, Meiner, Vardiella, additional, Basel‐Salmon, Lina, additional, Sagi‐Dain, Lena, additional, and Maya, Idit, additional

Published
2024
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20. Noncoding copy-number variations are associated with congenital limb malformation

Author

Flöttmann, Ricarda, Kragesteen, Bjørt K., Geuer, Sinje, Socha, Magdalena, Allou, Lila, Sowińska-Seidler, Anna, Bosquillon de Jarcy, Laure, Wagner, Johannes, Jamsheer, Aleksander, Oehl-Jaschkowitz, Barbara, Wittler, Lars, de Silva, Deepthi, Kurth, Ingo, Maya, Idit, Santos-Simarro, Fernando, Hülsemann, Wiebke, Klopocki, Eva, Mountford, Roger, Fryer, Alan, Borck, Guntram, Horn, Denise, Lapunzina, Pablo, Wilson, Meredith, Mascrez, Bénédicte, Duboule, Denis, Mundlos, Stefan, and Spielmann, Malte

Published
2018
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33. In Reply

Author

Sagi-Dain, Lena, Maya, Idit, Singer, Amihood, and Ben-Shachar, Shay

Published
2019
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34. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature

Author

Genetica Sectie Genoomdiagnostiek, CMM Groep Lens, Cancer, Child Health, Genetica Klinische Genetica, Brain, van Jaarsveld, Richard H, Reilly, Jack, Cornips, Marie-Claire, Hadders, Michael A, Agolini, Emanuele, Ahimaz, Priyanka, Anyane-Yeboa, Kwame, Bellanger, Severine Audebert, van Binsbergen, Ellen, van den Boogaard, Marie-Jose, Brischoux-Boucher, Elise, Caylor, Raymond C, Ciolfi, Andrea, van Essen, Ton A J, Fontana, Paolo, Hopman, Saskia, Iascone, Maria, Javier, Margaret M, Kamsteeg, Erik-Jan, Kerkhof, Jennifer, Kido, Jun, Kim, Hyung-Goo, Kleefstra, Tjitske, Lonardo, Fortunato, Lai, Abbe, Lev, Dorit, Levy, Michael A, Lewis, M E Suzanne, Lichty, Angie, Mannens, Marcel M A M, Matsumoto, Naomichi, Maya, Idit, McConkey, Haley, Megarbane, Andre, Michaud, Vincent, Miele, Evelina, Niceta, Marcello, Novelli, Antonio, Onesimo, Roberta, Pfundt, Rolph, Popp, Bernt, Prijoles, Eloise, Relator, Raissa, Redon, Sylvia, Rots, Dmitrijs, Rouault, Karen, Saida, Ken, Schieving, Jolanda, Tartaglia, Marco, Tenconi, Romano, Uguen, Kevin, Verbeek, Nienke, Walsh, Christopher A, Yosovich, Keren, Yuskaitis, Christopher J, Zampino, Giuseppe, Sadikovic, Bekim, Alders, Mariëlle, Oegema, Renske, Genetica Sectie Genoomdiagnostiek, CMM Groep Lens, Cancer, Child Health, Genetica Klinische Genetica, Brain, van Jaarsveld, Richard H, Reilly, Jack, Cornips, Marie-Claire, Hadders, Michael A, Agolini, Emanuele, Ahimaz, Priyanka, Anyane-Yeboa, Kwame, Bellanger, Severine Audebert, van Binsbergen, Ellen, van den Boogaard, Marie-Jose, Brischoux-Boucher, Elise, Caylor, Raymond C, Ciolfi, Andrea, van Essen, Ton A J, Fontana, Paolo, Hopman, Saskia, Iascone, Maria, Javier, Margaret M, Kamsteeg, Erik-Jan, Kerkhof, Jennifer, Kido, Jun, Kim, Hyung-Goo, Kleefstra, Tjitske, Lonardo, Fortunato, Lai, Abbe, Lev, Dorit, Levy, Michael A, Lewis, M E Suzanne, Lichty, Angie, Mannens, Marcel M A M, Matsumoto, Naomichi, Maya, Idit, McConkey, Haley, Megarbane, Andre, Michaud, Vincent, Miele, Evelina, Niceta, Marcello, Novelli, Antonio, Onesimo, Roberta, Pfundt, Rolph, Popp, Bernt, Prijoles, Eloise, Relator, Raissa, Redon, Sylvia, Rots, Dmitrijs, Rouault, Karen, Saida, Ken, Schieving, Jolanda, Tartaglia, Marco, Tenconi, Romano, Uguen, Kevin, Verbeek, Nienke, Walsh, Christopher A, Yosovich, Keren, Yuskaitis, Christopher J, Zampino, Giuseppe, Sadikovic, Bekim, Alders, Mariëlle, and Oegema, Renske

Published
2023

37. Proximal 1q21 duplication: A syndrome or a susceptibility locus?

Author

Levy, Michal, Shohat, Mordechai, Kahana, Sarit, Matar, Reut, Klein, Kochav, Fishman, Ifat Agmon, Gurevitch, Merav, Basel‐Salmon, Lina, and Maya, Idit

Abstract

Proximal 1q21 microduplication is an incomplete penetrance and variable expressivity syndrome. This study reports 28 new cases and summarizes data on phenotype, gender, and parental origin. Data on isolated proximal 1q21.1 microduplications (g. chr1:145,394,956–145,762,959 GRCh37/hg19) was retrieved in postnatal and prenatal "clinical cases" group, and prenatal "control group." The "clinical cases" cases included cases where chromosomal microarray (CMA) was performed due to congenital anomalies, autism spectrum disorder, seizures, and developmental delay/intellectual disability. The "control group" cases consisted of fetal CMA performed upon parental request despite normal nuchal translucency and anatomical second trimester fetal scans. We analyzed a local database of 27,990 cases and another cohort of 80,000 cases (including both indicated and non‐indicated cases) for population frequency analysis. A total of 62 heterozygous cases were found, including 28 index cases and 34 family members. Among the index cases, 13 (9 males, 4 females) were identified in the "clinical cases" group, of which 10 had developmental abnormalities. Parental origin was tested in 9/13 cases, and all were found to be maternally inherited. In the "control group," which comprised non‐affected cases, of 15 cases (10 males, 5 females), only 5/11 were maternally inherited. Four cases with clinical follow‐up showed no reported neurodevelopmental abnormalities. No de‐novo cases were detected, and the population frequency in both cohorts was 1:1000. Proximal 1q21.1 microduplication is a recurrent copy number variant, associated with neurodevelopmental abnormalities. It has a greater impact on males inheriting it from their mothers than females from their fathers. [ABSTRACT FROM AUTHOR]

Published
2023
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38. Prenatal microarray analysis in right aortic arch—a retrospective cohort study and review of the literature

Author

Maya, Idit, Singer, Amihood, Baris, Hagit N, Goldberg, Yael, Shalata, Adel, Khayat, Morad, Ben-Shachar, Shay, and Sagi-Dain, Lena

Abstract

To examine the risk for clinically significant chromosomal microarray analysis (CMA) findings in fetal right aortic arch (RAA). Data from all CMA analyses performed owing to isolated RAA reported to the Israeli Ministry of Health between January 2013 and September 2016 were evaluated retrospectively. Risk for abnormal CMA findings was compared with two control populations, based on both previously described 9272 pregnancies with normal ultrasound, and on a local cohort of 5541 pregnancies undergoing CMA testing owing to maternal request. In addition, Pubmed database search was conducted for original researches examining this issue. Of 94 CMA analyses performed owing to isolated RAA, six (6.4%) pathogenic findings were detected (47,XX?+?21; 45,X; two 22q11.2 microdeletions; 10p15.3 microdeletion and 16p11.2 duplication). Compared with control groups, an isolated RAA yielded a significantly increased relative risk for abnormal CMA results. Literature search yielded two additional retrospective studies describing microarray testing in RAA and encompassing 57 cases. The overall risk for clinically significant CMA findings was 6.62% (10/151). CMA testing is indicated in cases of prenatal isolated RAA, even in the era of advanced sonographic equipment, routine biochemical screening for Down syndrome and available non-invasive prenatal testing.

Published
2024
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40. Homozygous MED25 mutation implicated in eye–intellectual disability syndrome

Author

Basel-Vanagaite, Lina, Smirin-Yosef, Pola, Essakow, Jenna Lee, Tzur, Shay, Lagovsky, Irina, Maya, Idit, Pasmanik-Chor, Metsada, Yeheskel, Adva, Konen, Osnat, Orenstein, Naama, Weisz Hubshman, Monika, Drasinover, Valerie, Magal, Nurit, Peretz Amit, Gaby, Zalzstein, Yael, Zeharia, Avraham, Shohat, Mordechai, Straussberg, Rachel, Monté, Didier, Salmon-Divon, Mali, and Behar, Doron M.

Published
2015
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43. Residual risk for clinically significant copy number variants in low-risk pregnancies, following exclusion of noninvasive prenatal screening–detectable findings

Author

Maya, Idit, primary, Salzer Sheelo, Liat, additional, Brabbing-Goldstein, Dana, additional, Matar, Reut, additional, Kahana, Sarit, additional, Agmon-Fishman, Ifaat, additional, Klein, Cochava, additional, Gurevitch, Merav, additional, Basel-Salmon, Lina, additional, and Sagi-Dain, Lena, additional

Published
2022
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46. SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system

Author

Birk, Efrat, Har-Zahav, Adi, Manzini, Chiara M., Pasmanik-Chor, Metsada, Kornreich, Liora, Walsh, Christopher A., Noben-Trauth, Konrad, Albin, Adi, Simon, Amos J., Colleaux, Laurence, Morad, Yair, Rainshtein, Limor, Tischfield, David J., Wang, Peter, Magal, Nurit, Maya, Idit, Shoshani, Noa, Rechavi, Gideon, Gothelf, Doron, Maydan, Gal, Shohat, Mordechai, and Basel-Vanagaite, Lina

Subjects
Cognition -- Analysis, Gene expression -- Analysis, Gene mutations -- Analysis, Mental illness -- Genetic aspects, Biological sciences
Abstract

The identification of a truncating mutation in the protein encoded by the SOBP that is responsible for causing both syndromic and nonsyndromic intellectual disability (ID) in the same family is reported. SOBP, a gene involved in human cognition is found to be the highest expression in the limbic system postnatally which on mutation causes syndromic and nonsyndromic autosomal-recessive ID.

Published
2010

48. RIN2 deficiency results in macrocephaly, alopecia, cutis laxa, and scoliosis: MACS syndrome

Author

Basel-Vanagaite, Lina, Sarig, Ofer, Hershkovitz, Dov, Fuchs-Telern, Dana, Rapaport, Debora, Gat, Andrea, Isman, Gila, Shirazi, Idit, Shohat, Mordechai, Enk, Claes D., Birk, Efrat, Kohlhase, Jurgen, Matysiak-Scholze, Uta, Maya, Idit, Knopf, Carlos, Peffekoven, Anette, Hennies, Hans-Christian, Bergman, Reuven, Horowitz, Mia, Ishida-Yamamoto, Akemi, and Sprecher, Eli

Subjects
Human genome -- Research, Macrocephaly -- Genetic aspects, Macrocephaly -- Physiological aspects, Alopecia -- Genetic aspects, Baldness -- Genetic aspects, Cutis laxa -- Genetic aspects, Gene mutations -- Analysis, Biological sciences
Abstract

A study aims to identify the causative gene which is associated with an autosomal-recessive disorder known as MACS syndrome, characterized by abnormal skin phenotypes such as macrocephaly, alopecia, cutis laxa, and scoliosis in humans. Results reveal that a homozygous frameshift mutation in the RIN2 gene located at chromosome 20p11.21-p11.23 results in the deficiency of RIN2 protein, which is expressed as MACS syndrome.

Published
2009

49. Homozygous MED25 mutation implicated in eye-intellectual disability syndrome

Author

Basel-Vanagaite, Lina, Smirin-Yosef, Pola, Essakow, Jenna, Tzur, Shay, Lagovsky, Irina, Maya, Idit, Pasmanik-Chor, Metsada, Yeheskel, Adva, Konen, Osnat, Orenstein, Naama, Weisz Hubshman, Monika, Drasinover, Valerie, Magal, Nurit, Peretz Amit, Gaby, Zalzstein, Yael, Zeharia, Avraham, Shohat, Mordechai, Straussberg, Rachel, Monté, Didier, Salmon-Divon, Mali, Behar, Doron, Basel-Vanagaite, Lina, Smirin-Yosef, Pola, Essakow, Jenna, Tzur, Shay, Lagovsky, Irina, Maya, Idit, Pasmanik-Chor, Metsada, Yeheskel, Adva, Konen, Osnat, Orenstein, Naama, Weisz Hubshman, Monika, Drasinover, Valerie, Magal, Nurit, Peretz Amit, Gaby, Zalzstein, Yael, Zeharia, Avraham, Shohat, Mordechai, Straussberg, Rachel, Monté, Didier, Salmon-Divon, Mali, and Behar, Doron

Abstract

Genetic syndromes involving both brain and eye abnormalities are numerous and include syndromes such as Warburg micro syndrome, Kaufman oculocerebrofacial syndrome, Cerebro-oculo-facio-skeletal syndrome, Kahrizi syndrome and others. Using exome sequencing, we have been able to identify homozygous mutation p.(Tyr39Cys) in MED25 as the cause of a syndrome characterized by eye, brain, cardiac and palatal abnormalities as well as growth retardation, microcephaly and severe intellectual disability in seven patients from four unrelated families, all originating from the same village. The protein encoded by MED25 belongs to Mediator complex or MED complex, which is an evolutionary conserved multi-subunit RNA polymerase II transcriptional regulator complex. The MED25 point mutation is located in the von Willebrand factor type A (MED25 VWA) domain which is responsible for MED25 recruitment into the Mediator complex; co-immunoprecipitation experiment demonstrated that this mutation dramatically impairs MED25 interaction with the Mediator complex in mammalian cells.

Published
2021

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