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Navarrete-Meneses MP, Ochoa-Mellado I, Gutiérrez-Álvarez R, Martínez-Anaya D, Juárez-Figueroa U, Durán-McKinster C, Lieberman-Hernández E, Yokoyama-Rebollar E, Gómez-Carmona S, Del Castillo-Ruiz V, Pérez-Vera P, Salas-Labadía C. Cytogenomic characterization of small supernumerary marker chromosomes in patients with pigmentary mosaicism. Front Genet 2024; 15:1356786. [PMID: 38711916 PMCID: PMC11071077 DOI: 10.3389/fgene.2024.1356786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/21/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction The combination of gene content on the marker chromosome, chromosomal origin, level of mosaicism, origin mechanism (chromothripsis), and uniparental disomy can influence the final characterization of sSMCs. Several chromosomal aberrations, including sSMCs, have been observed in 30%-60% of patients with pigmentary mosaicism, and in more than 80%, chromosomal abnormalities are present in the mosaic state. In patients with pigmentary mosaicism the most representative chromosomes involved in sSMCs are 3, 5, 6, 9, 10, 13, 15, 18, 20, and X. In this study, we included the complete clinical, cytogenetic, and molecular characterization of seven patients with pigmentary mosaicism associated with the presence of SMCs of different chromosomal origins. Methods The patients were diagnosed by the Genetics and Dermatology Department of three different hospitals. Cytogenetic and FISH analyses were performed on peripheral blood, light skin, and dark skin. FISH analysis was performed using different probes, depending on the marker chromosome description. Different array analysis was performed. Results To date, of the seven cases studied, the chromosomal origins of six were successfully identified by FISH or array analysis. The chromosomes involved in SMCs were 6, 9, 15, and 18, X. The most frequently found was the centric minute structure. Discussion To date, this group of seven patients constitutes the largest clinical and cytogenetically finely described study of cases with pigmentary mosaicism associated with sSMCs. Undoubtedly, analysis of the two skin types is a fundamental part of our study, as numerical differences may occur in the cell lines found in each skin type. The knowledge generated in this study will help delineate a very heterogeneous entity more accurately, and in the future, analyzing more patients with PM will likely establish a more definite association with the presence of this genetic alteration.
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Affiliation(s)
- M. P. Navarrete-Meneses
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - I. Ochoa-Mellado
- Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - R. Gutiérrez-Álvarez
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - D. Martínez-Anaya
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - U. Juárez-Figueroa
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - C. Durán-McKinster
- Departamento de Dermatología, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | | | - S. Gómez-Carmona
- Departamento de Genética Médica, Centro de Rehabilitación e Inclusión Infantil Teletón, Cancún, México
| | | | - P. Pérez-Vera
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - C. Salas-Labadía
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
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Xue H, Guo Q, Yu A, Lin M, Chen X, Xu L. Genetic analysis of chorionic villus tissues in early missed abortions. Sci Rep 2023; 13:21719. [PMID: 38081877 PMCID: PMC10713591 DOI: 10.1038/s41598-023-48358-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Chromosomal abnormalities are the most common etiology of early spontaneous miscarriage. However, traditional karyotyping of chorionic villus samples (CVSs) is limited by cell culture and its low resolution. The objective of our study was to investigate the efficiency of molecular karyotyping technology for genetic diagnosis of early missed abortion tissues. Chromosome analysis of 1191 abortion CVSs in early pregnancy was conducted from August 2016 to June 2021; 463 cases were conducted via copy-number variations sequencing (CNV-seq)/quantitative fluorescent-polymerase chain reaction (QF-PCR) and 728 cases were conducted using SNP array. Clinically significant CNVs of CVSs were identified to clarify the cause of miscarriage and to guide the couples' subsequent pregnancies. Among these, 31 cases with significant maternal cell contamination were removed from the study. Among the remaining 1160 samples, 751 cases (64.7%) with genetic abnormalities were identified, of which, 531 (45.8%) were single aneuploidies, 31 (2.7%) were multiple aneuploidies, 50 (4.3%) were polyploidies, 54 (4.7%) were partial aneuploidies, 77 (6.6%) had submicroscopic CNVs (including 25 with clinically significant CNVs and 52 had variants of uncertain significance), and 8 cases (0.7%) were uniparental disomies. Our study suggests that both SNP array and CNV-seq/QF-PCR are reliable, robust, and high-resolution technologies for genetic diagnosis of miscarriage.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China.
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China.
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Yao TY, Wu WJ, Law KS, Lee MH, Chang SP, Lee DJ, Lin WH, Chen M, Ma GC. Prenatal Diagnosis of True Fetal Mosaicism with Small Supernumerary Marker Chromosome Derived from Chromosome 16 by Funipuncture and Molecular Cytogenetics Including Chromosome Microarray. Diagnostics (Basel) 2021; 11:diagnostics11081457. [PMID: 34441391 PMCID: PMC8391486 DOI: 10.3390/diagnostics11081457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023] Open
Abstract
This study examined the molecular characterization of a prenatal case with true fetal mosaicism of small supernumerary marker chromosome 16 (sSMC(16)). A 41-year-old female underwent amniocentesis at 19 weeks of gestation due to advanced maternal age. Chromosomal analysis for cultured amniocytes revealed a karyotype of 47,XY,+mar[4]/46,XY[16]. Spectral karyotyping and metaphase fluorescence in situ hybridization (FISH) demonstrated that the sSMC was derived from chromosome 16 (47,XY,+mar.ish der(16)(D16Z1+)[13/20]). Confined placental mosaicism was initially suspected because the prenatal ultrasound revealed a normal structure and the pregnancy was uneventful. However, interphase FISH of cord blood performed at 28 weeks of gestation showed 20% mosaicism of trisomy chromosome 16 (nuc ish(D16Z2×3)[40/200]). Chromosome microarray analysis further demonstrated 55% mosaicism of an 8.02 Mb segmental duplication at the subcentromeric region of 16p12.1p11.1 (arr[GRCh37] 16p12.1p11.1(27021975_35045499)×3[0.55]). The results demonstrated a true fetal mosaicism of sSMC(16) involving chromosome16p12.1p11.1 that is associated with chromosome 16p11.2 duplication syndrome (OMIM #614671). After non-directive genetic counseling, the couple opted for late termination of pregnancy. This case illustrated the use of multiple molecular cytogenetic tools to elucidate the origin and structure of sSMC, which is crucial for prenatal counseling, decision making, and clinical management.
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Affiliation(s)
- Tien-Yu Yao
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua 50006, Taiwan; (T.-Y.Y.); (W.-J.W.)
| | - Wan-Ju Wu
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua 50006, Taiwan; (T.-Y.Y.); (W.-J.W.)
- PhD Programs in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan; (M.-H.L.); (S.-P.C.)
| | - Kim-Seng Law
- Department of Obstetrics and Gynecology, Tung’s Taichung MetroHarbor Hospital, Taichung 43344, Taiwan;
- Department of Nursing, Jenteh Junior College of Medicine, Nursing and Management, Miaoli 35665, Taiwan
- Department of Life Science, National Chung Hsin University, Taichung 40227, Taiwan
| | - Mei-Hui Lee
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan; (M.-H.L.); (S.-P.C.)
| | - Shun-Ping Chang
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan; (M.-H.L.); (S.-P.C.)
| | - Dong-Jay Lee
- Research Department, Changhua Christian Hospital, Changhua 50006, Taiwan;
| | - Wen-Hsiang Lin
- Welgene Biotechnology Company, Nangang Business Park, Taipei 11503, Taiwan;
| | - Ming Chen
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua 50006, Taiwan; (T.-Y.Y.); (W.-J.W.)
- PhD Programs in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan; (M.-H.L.); (S.-P.C.)
- Research Department, Changhua Christian Hospital, Changhua 50006, Taiwan;
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei 10041, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10041, Taiwan
- Department of Molecular Biotechnology, Da-Yeh University, Changhua 51591, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Gwo-Chin Ma
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua 50046, Taiwan; (M.-H.L.); (S.-P.C.)
- Research Department, Changhua Christian Hospital, Changhua 50006, Taiwan;
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Mohammadi R, Taheri R, Shahriyari F, Feiz F, Mohammadi Z, Shirian S, Raoofian R, Malekpour A, Pazhoomand R. Prenatal diagnosis of de novo small supernumerary marker chromosome 4q (4q11-q12): A case report. Int J Reprod Biomed 2021; 19:477-482. [PMID: 34278202 PMCID: PMC8261101 DOI: 10.18502/ijrm.v19i5.9258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/06/2020] [Accepted: 10/06/2020] [Indexed: 11/28/2022] Open
Abstract
Background Small supernumerary marker chromosomes (sSMCs) are chromosomal fragments with
abnormal structures found in patients with fertility problems and
developmental delay. They may be detected in amniotic cell karyotypes. sSMCs
are categorized as hereditary or de novo. Here, we describe a case of
prenatal de novo 4q11q12 sSMC and its molecular cytogenetic features which
had no apparent phenotypic abnormality. Case The fetus of a 36-yr-old pregnant woman was detected positive for Down's
syndrome (trisomy 21) at the 16 th wk of gestation. Quantitative fluorescent polymerase chain
reaction technique was applied for the rapid detection of numerical
aneuploidy of chromosomes X, Y, 13, 18, and 21 microsatellites. Array
comparative genomic hybridization (array CGH) technique was also conducted
following the karyotype analysis of amniotic cells. The karyotype analysis
was also done for the parents. Quantitative fluorescent polymerase chain
reaction result revealed a male fetus with a normal chromosomal pattern,
while the amniocentesis karyotype analysis identified a male fetus with a
marker chromosome (47, XY, +mar), and the sSMC were existing in 100% of
amniocyte metaphase spreads. The parents' normal karyotypes indicated that
the sSMC was de novo. Array CGH analysis revealed a 6.48-Mb duplication at
4q11q12. Eventually, the parents decided to terminate the pregnancy by legal
abortion. Conclusion Our study highlights the importance of the application of array CGH in
combination with karyotype analysis for rapid and precise prenatal diagnosis
of partial aneuploidy region.
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Affiliation(s)
- Reza Mohammadi
- Genetic Laboratory, Shiraz Fertility Center, Zargari St., Shiraz, Iran
| | - Raheleh Taheri
- Genetic Laboratory, Shiraz Fertility Center, Zargari St., Shiraz, Iran
| | | | - Farnaz Feiz
- Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Mohammadi
- Pathobiology Laboratory of Ordibehesht Hospital, Shiraz, Iran
| | - Sadegh Shirian
- Department of Pathology, School of Veterinary Medicine, Shahrekord University, Shahrekord, Iran.,Shiraz Molecular Pathology Research Center, Dr Daneshbod Pathol Lab, Shiraz, Iran.,Shefa Neurosciences Research Center, Tehran, Iran
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | | | - Reza Pazhoomand
- Genetic Laboratory, Shiraz Fertility Center, Zargari St., Shiraz, Iran.,Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
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Detection of copy number variation associated with ventriculomegaly in fetuses using single nucleotide polymorphism arrays. Sci Rep 2021; 11:5291. [PMID: 33674646 PMCID: PMC7935846 DOI: 10.1038/s41598-021-83147-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/28/2021] [Indexed: 11/08/2022] Open
Abstract
Etiopathogenesis of fetal ventriculomegaly is poorly understood. Associations between fetal isolated ventriculomegaly and copy number variations (CNVs) have been previously described. We investigated the correlations between fetal ventriculomegaly-with or without other ultrasound anomalies-and chromosome abnormalities. 222 fetuses were divided into four groups: (I) 103 (46.4%) cases with isolated ventriculomegaly, (II) 41 (18.5%) cases accompanied by soft markers, (III) 33 (14.9%) cases complicated with central nervous system (CNS) anomalies, and (IV) 45 (20.3%) cases with accompanying anomalies. Karyotyping and single nucleotide polymorphism (SNP) array were used in parallel. Karyotype abnormalities were identified in 15/222 (6.8%) cases. Karyotype abnormalities in group I, II, III, and IV were 4/103 (3.9%), 2/41 (4.9%), 4/33 (12.1%), and 5/45 (11.1%), respectively. Concerning the SNP array analysis results, 31/222 (14.0%) were CNVs, CNVs in groups I, II, III, and IV were 11/103 (10.7%), 6/41 (14.6%), 9/33 (27.3%), and 5/45 fetuses (11.1%), respectively. Detections of clinical significant CNVs were higher in non-isolated ventriculomegaly than in isolated ventriculomegaly (16.81% vs 10.7%, P = 0.19). SNP arrays can effectively identify CNVs in fetuses with ventriculomegaly and increase the abnormal chromosomal detection rate by approximately 7.2%, especially ventriculomegaly accompanied by CNS anomalies.
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The Cytogenomic "Theory of Everything": Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging. Int J Mol Sci 2020; 21:ijms21218328. [PMID: 33171981 PMCID: PMC7664247 DOI: 10.3390/ijms21218328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/28/2023] Open
Abstract
Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are not completely understood. During molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n = 612), we observed colocalization of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n = 47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek words chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either in partial/whole chromosome loss (e.g., aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g., prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything”, similar to the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.
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Zhuang J, Wang Y, Zeng S, Lv C, Lin Y, Jiang Y. A prenatal diagnosis and genetics study of five pedigrees in the Chinese population with Xp22.31 microduplication. Mol Cytogenet 2019; 12:50. [PMID: 31857824 PMCID: PMC6907354 DOI: 10.1186/s13039-019-0461-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022] Open
Abstract
Background Copy number variations (CNVs) can contribute to human phenotype, phenotypic diversity and disease susceptibility, while others may benign. In the current study, an attempt to investigate the pathogenicity of CNVs in chromosome Xp22.31 was explored. Methods G-banding and SNP-array techniques were used to analyze chromosome karyotypes and CNVs in fetuses. Parents associate with five different pedigrees possessing high risk factors in pregnancy were considered with such parameters as advanced age, high risk of serological screening and ultrasound abnormalities. Results The fetuses’ amniotic fluid karyotypes were 46, XX and those of their parents with the five pedigrees revealed no abnormalities. Here, we noticed a series of individuals with Xp22.31 duplications ranging from 534.6 kb to 1.6 Mb. It was detected through SNP array that the fetuses in Pedigree 1 and 2 had ~ 600 kb duplications in the Xp22.31 region of their X chromosomes which contained two OMIM genes, HDHD1 (OMIM: 306480) and part of STS (OMIM: 300747). The fetuses of Pedigrees 3, 4 and 5 had 1.6 Mb duplication in the same chromosome which contained four OMIM genes: HDHD1 (OMIM: 306480), STS (OMIM: 300747), PNPLA4 (OMIM: 300102) and VCX (OMIM: 300229). The duplications in the fetuses of Pedigrees 1 and 5 were inherited from the non-phenotypic parents. Pedigrees 3 and 4 refused to perform parental verification. Finally, four of the five pedigrees continue towards pregnancy with no abnormalities being observed during followed-ups. Conclusion Our study first showed duplications of Xp22.31 in Chinese population. Clinical and genetic investigation on five different pedigrees, we consider the duplication of these fragments as likely benign copy number variants (CNVs). We suggest that the duplications of Xp22.31 with recurrent duplication as a benign CNVs .
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Shuhong Zeng
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Chunling Lv
- Zhejiang Biosan technology Co., Ltd, Zhejiang, People's Republic of China
| | - Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Fujian Province, People's Republic of China
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Costa JA, Dentinger PM, McGall GH, Crnogorac F, Zhou W. Fabrication of Inverted High-Density DNA Microarrays in a Hydrogel. ACS APPLIED MATERIALS & INTERFACES 2019; 11:30534-30541. [PMID: 31389236 DOI: 10.1021/acsami.9b07755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current techniques for making high-resolution, photolithographic DNA microarrays suffer from the limitation that the 3' end of each sequence is anchored to a hard substrate and hence is unavailable for many potential enzymatic reactions. Here, we demonstrate a technique that inverts the entire microarray into a hydrogel. This method preserves the spatial fidelity of the original pattern while simultaneously removing incorrectly synthesized oligomers that are inherent to all other microarray fabrication strategies. First, a standard 5'-up microarray on a donor wafer is synthesized, in which each oligo is anchored with a cleavable linker at the 3' end and an Acrydite phosphoramidite at the 5' end. Following the synthesis of the array, an acrylamide monomer solution is applied to the donor wafer, and an acrylamide-silanized acceptor wafer is placed on top. As the polyacrylamide hydrogel forms between the two wafers, it covalently incorporates the acrydite-terminated sequences into the matrix. Finally, the oligos are released from the donor wafer upon immersing in an ammonia solution that cleaves the 3'-linkers, thus freeing the oligos at the 3' end. The array is now presented 3'-up on the surface of the gel-coated acceptor wafer. Various types of on-gel enzymatic reactions demonstrate a versatile and robust platform that can easily be constructed with far more molecular complexity than traditional photolithographic arrays by endowing the system with multiple enzymatic substrates. We produce a new generation of microarrays where highly ordered, purified oligos are inverted 3'-up, in a biocompatible soft hydrogel, and functional with respect to a wide variety of programable enzymatic reactions.
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Affiliation(s)
- Justin A Costa
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Paul M Dentinger
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Glenn H McGall
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Filip Crnogorac
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
| | - Wei Zhou
- Centrillion Technologies , 2500 Faber Place , Palo Alto , California 94303 , United States
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