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single nucleotide polymorphism array (SNP-array) analysis for fetuses with abnormal nasal bone

ARCHIVES OF GYNECOLOGY AND OBSTETRICS 2024年第6期309卷 2475-2482页

作者： Xie, Xiaorui Su, Linjuan Li, Ying Shen, Qingmei Wang, Meiying Wu, Xiaoqing Fujian Med Univ Fujian Prov Matern & Childrens Hosp Med Genet Diag & Therapy Ctr Fujian Key Lab Prenatal Diag & Birth DefectAffili 18 Daoshan Rd Fuzhou 350001 Peoples R China

PurposeThis study aims to evaluate the prevalence of submicroscopic chromosomal abnormalities found on single nucleotide polymorphism array (SNP array) in pregnancies with either an absent or hypoplastic nasal *** retrospective study included 333 fetuses with either nasal bone hypoplasia or absence identified on prenatal ultrasound. SNP array analysis and conventional karyotyping were performed in all the subjects. The prevalence of chromosomal abnormalities was adjusted for maternal age and other ultrasound findings. Fetuses with either an isolated nasal bone absence or hypoplasia, those that had additional soft ultrasound markers, and those where structural defects were found on ultrasound were divided into three groups: A, B, and C, *** the total cohort of 333 fetuses, 76 (22.8%) had chromosomal abnormalities, including 47 cases of trisomy 21, 4 cases of trisomy 18, 5 cases of sex chromosome aneuploidy, and 20 cases of copy number variations of which 12 were pathogenic or likely pathogenic. The prevalence of chromosomal abnormalities in group A (n = 164), B (n = 79), and C (n = 90) was 8.5%, 29.1% and 43.3%, respectively. The incremental yields by SNP-array compared with karyotyping in group A, B, and C were 3.0%, 2.5% and 10.7%, respectively (p > 0.05). Compared to karyotype analysis, SNP array detected an additional 2 (1.2%), 1 (1.3%), and 5 (5.6%) pathogenic or likely pathogenic CNVs in groups A, B, and C, respectively. In the 333 fetuses, the prevalence of chromosomal abnormalities in women with advanced maternal age (AMA) was significantly higher than that in non-AMA women, (47.8% vs. 16.5%, p < 0.05).ConclusionIn addition to Down's syndrome, many other chromosomal abnormalities are present in fetuses with abnormal nasal bone. SNP array can improve the prevalence of chromosomal abnormalities associated with nasal bone abnormalities, especially in pregnancies with non-isolated nasal bone abnormalities and advanced maternal a

关键词： Nasal bone absence Nasal bone hypoplasia Karyotyping single nucleotide polymorphism array Copy number variations

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single nucleotide polymorphism array analysis of 102 patients with developmental delay and/or intellectual disability from Fujian, China

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CLINICA CHIMICA ACTA 2020年 510卷 638-643页

作者： Liang, Bin Wang, Yan Lin, Na Huang, Hailong Chen, Lingji Chen, Meihuan Yu, Donghong Chen, Xuemei He, Deqin Xu, Liangpu Fujian Med Univ Fujian Matern & Child Hlth Hosp Fujian Key Lab Prenatal Diag & Birth Defect Affiliated Hosp Fuzhou 350001 Peoples R China Fujian Med Univ Fujian Matern & Child Hlth Hosp Med Res Ctr Affiliated Hosp Fuzhou 350001 Peoples R China

Developmental delay/intellectual disability (DD/ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In this study, we evaluated the usefulness of single nucleotide polymorphism (SNP) array in the detection of genetic causes of 102 DD/ID patients from Fujian (China). Of them, clinically relevant variants (including pathogenic and likely pathogenic), variants of uncertain significance (VOUS), and no clinically relevant variants (including likely benign and benign) were detected in 19, 4 and 79 patients, accounting for 18.6%, 3.9% and 77.5%, respectively, with a diagnostic yield of 18.6% in our study. Furthermore, we divided 19 clinically relevant variants into 4 groups, including chromosome aneuploidy (n = 1);large copy number variants (CNVs) (> 10 Mb) (n = 8);known genomic disorders (n = 8), and likely pathogenic CNVs (n = 2). Moreover, we discussed our findings with respect to 4 cases of VOUS. Overall, we confirmed that DD/ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide SNP array in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with causal chromosomal aberrations, and discussed the potential implication in DD/ID of genes located within those CNVs or regions of homozygosity.

关键词： Developmental delay Intellectual disability single nucleotide polymorphism array Copy number variant Region of homozygosity

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Pedigree reconstruction for triploid apple cultivars using single nucleotide polymorphism array data

PLANTS PEOPLE PLANET

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PLANTS PEOPLE PLANET 2023年第1期5卷 98-111页

作者： Howard, Nicholas P. Micheletti, Diego Luby, James J. Durel, Charles-Eric Denance, Caroline Muranty, Helene Ordidge, Matthew Albach, Dirk C. Carl von Ossietzky Univ Oldenburg Inst Biol & Umweltwissensch Oldenburg Germany Univ Minnesota Dept Hort Sci St Paul MN 55108 USA Fdn Edmund Mach San Michele All Adige TN Italy Univ Angers Inst Agro SFR QuaSaV INRAEIRHS Angers France Univ Reading Sch Agr Policy & Dev Reading Berks England

Societal Impact Statement Many economically, culturally, and historically important apple cultivars are triploids, which have three copies of each chromosome instead of the more typical two copies in diploids. Despite their prevalence and importance, there have been conflicting reports regarding their origin and their ability to beget diploids. New genetic analysis methodologies outlined in this study have clarified the genetic origin of triploid apple cultivars and suggest that triploidy has been a dead end in historic apple pedigrees. The specific results of this study have resolved the pedigrees of many cultivars, including the famous English cultivar Cox's Orange Pippin and the oldest known US cultivar Roxbury Russet. In apple (Malus x domestica), most cultivars are diploid, though a sizeable number are triploids, which tend to be stronger growing, more robust, and bear larger fruit. However, triploidy is also associated with strongly reduced fertility. Some recorded pedigrees for historical apple cultivars include triploids as parents of diploids, despite this reputation of poor fertility. This information, coupled with some initiatives using triploids in breeding efforts, result in confusion about how possible or common it is for triploids to be parents of diploid offspring. To date, no studies have systematically evaluated and identified pedigrees of triploid apple cultivars to resolve these contradictions. Here, we describe a method to make triploid genotype calls using Illumina Infinium single nucleotide polymorphism (SNP) array data through a novel Python script: ploidyClassifier. SNP data for 219 unique triploids was compared alongside 2498 unique diploid apple accessions to conduct pedigree reconstruction. Unreduced gamete-donating parents were identified for over half of the triploid accessions. From those, reduced gamete-donating parents were identified for nearly half. Full or partial pedigrees for many classic triploids were uncovered, including that

关键词： apple genetics Malus pedigree reconstruction polyploidy single nucleotide polymorphism array triploid

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Concurrent exome-targeted next-generation sequencing and single nucleotide polymorphism array to identify the causative genetic aberrations of isolated Mayer-Rokitansky-Kuster-Hauser syndrome

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HUMAN REPRODUCTION 2015年第7期30卷 1732-1742页

作者： Chen, Mei-Jou Wei, Shin-Yi Yang, Wei-Shiung Wu, Tsai-Tzu Li, Huei-Ying Ho, Hong-Nerng Yang, Yu-Shih Chen, Pei-Lung Natl Taiwan Univ Hosp Dept Obstet & Gynecol Taipei 100 Taiwan Natl Taiwan Univ Hosp Dept Internal Med Taipei 100 Taiwan Natl Taiwan Univ Grad Inst Clin Med Coll Med Taipei 100 Taiwan Natl Taiwan Univ Res Ctr Dev Biol & Regenerat Med Taipei 100 Taiwan Natl Taiwan Univ Grad Inst Mol Med Coll Med Taipei 100 Taiwan Natl Taiwan Univ Hosp Dept Med Genet Taipei 100 Taiwan Natl Taiwan Univ Coll Med Grad Inst Med Genom & Prote Taipei 100 Taiwan

STUDY QUESTION: Can the use of whole-exome sequencing (WES) together with single nucleotide polymorphism (SNP) array help to identify novel causative genes of isolated Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome? SUMMARY ANSWER: OR4M2 (olfactory receptor, family 4, subfamily M, member 2) and PDE11A (phosphodiesterase 11A) gene loss-of-function variants as well as deletions at 15q11.2, 19q13.31, 1p36.21, and 1q44 were identified as possible commonly altered regions in patients with type 1 MRKH. WHAT IS KNOWN ALREADY: The isolated form of Mullerian aplasia is the most common subtype of MRKH syndrome, which invariably leads to difficulties producing offspring in affected women. However, there is little information currently available to allow for genetic testing and counseling to be performed for those affected by this syndrome. STUDY DESIGN, SIZE AND DURATION: This was a case-series genetic study. A total of seven consecutive unrelated women with type 1 MRKH were enrolled. The enrollment and experimental procedures were performed over a 2-year period. PARTICIPANTS/MATERIALS, SETTING, METHODS: Whole exome-targeted next-generation sequencing and SNP array (Affymetrix Genome-Wide Human SNP array 6.0) were performed on the first five unrelated women with type 1 MRKH syndrome. The data were combined, and the '3-hit principal' was applied on a genome-wide scale to search for the common causative genes. Quantitative PCR (qPCR) and Sanger sequencing were used to validate the identified genomic copy number losses and variants. Replication tests using direct Sanger sequencing and qPCR were performed on the remaining two women with type 1 MRKH syndrome to support the credibility of the potential candidate genes and deletions. MAIN RESULTS AND THE ROLE OF CHANCE: A total of 3443 damaging variants based on WES were shown to intersect with 1336 copy number variations (deletions) derived from the SNP array. Four highly recurrent deletions at 15q11.2 (80%), 19q13.31 (40%), 1p36.21

关键词： next-generation sequencing whole-exome sequencing single nucleotide polymorphism array Mayer-Rokitansky-Kuster-Hauser syndrome Mullerian aplasia

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Prenatal diagnosis of 22q11.2 copy number abnormalities in fetuses via single nucleotide polymorphism array

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MOLECULAR BIOLOGY REPORTS 2020年第10期47卷 7529-7535页

作者： Cai, Meiying Lin, Na Su, Linjuan Wu, Xiaoqing Xie, Xiaorui Li, Ying Lin, Yuan Huang, Hailong Xu, Liangpu Fujian Med Univ Fujian Key Lab Prenatal Diag & Birth Defect Fujian Matern & Child Hlth Hosp Dept Prenatal Diag CtrAffiliated Hosp Fuzhou Peoples R China

The q11.2 region on chromosome 22 contains numerous low-copy repeats that lead to deleted or duplicated regions in the chromosome, thereby resulting in different syndromes characterized by intellectual disabilities or congenital anomalies. The association between patient phenotypes and 22q11.2 copy number abnormalities has been previously described in postnatal cases;however, these features have not been systematically evaluated in prenatal cases because of limitations in phenotypic identification in prenatal testing. In this study, we investigated the detection rate of 22q11.2 copy number abnormalities in 2500 fetuses using single nucleotide polymorphism (SNP) array and determined the common abnormal ultrasound findings in fetuses carrying the 22q11.2 copy number abnormalities. The 22q11.2 copy number abnormalities were identified in 13 fetuses with cardiovascular malformations (6/13), kidney malformations (3/13), isolated ultrasound markers (3/13), or high-risk Down syndrome based on maternal serum screening (1/13). Approximately 0.5% (13/2500) of the fetuses harbored 22q11.2 copy number abnormalities. The most frequent ultrasound findings in fetuses with these abnormalities were cardiovascular malformations, followed by kidney malformations and isolated ultrasound markers. Prenatal diagnosis of these genetic abnormalities allows for the delineation of differential diagnoses, characterization of a wide spectrum of associated malformations, and determination of associations that exist between prenatal diagnosis and obstetrical outcomes.

关键词： 22q11 2 copy number abnormality single nucleotide polymorphism array Prenatal diagnosis Genomic diseases

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Whole-Genome single nucleotide polymorphism array Analysis Is Complementary to Classical Cytogenetic Analysis in the Evaluation of Lymphoid Proliferations

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AMERICAN JOURNAL OF CLINICAL PATHOLOGY 2014年第2期141卷 247-255页

作者： Gibson, Sarah E. Luo, Jianhua Sathanoori, Malini Liao, Jun Surti, Urvashi Swerdlow, Steven H. Univ Pittsburgh Sch Med Dept Pathol Pittsburgh PA USA UPMC Magee Womens Hosp Pittsburgh Cytogenet Lab Pittsburgh PA 15213 USA

Objectives: To explore how much additional information single nucleotide polymorphism (SNP) arrays provide and whether they could partially replace classical cytogenetics. Methods: Twenty-six lymphoid proliferations with available cytogenetic studies were analyzed with the Affymetrix Genome-Wide Human SNP array 6.0 (Affymetrix, Santa Clara, CA). Results: Eleven of 26 cases demonstrated complete concordance between cytogenetics and SNP analysis, and 10 of 26 cases demonstrated partial concordance. Five discordant cases had copy number abnormalities (CNAs) with cytogenetics not identified with SNP arrays. While SNP analysis showed CNAs not apparent by cytogenetics in eight cases and helped clarify the karyotype in six cases, cytogenetics demonstrated CNAs not seen by SNP analysis in 15 cases as well as balanced translocations in 12 cases. Conclusions: The combination of cytogenetics and SNP analysis results in a higher overall yield in identifying numerical chromosomal abnormalities than either technique alone.

关键词： single nucleotide polymorphism array SNP Classical cytogenetics Lymphoma Lymphoid proliferations

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Improved assay performance of single nucleotide polymorphism array over conventional karyotyping in analyzing products of conception

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JOURNAL OF THE CHINESE MEDICAL ASSOCIATION 2015年第7期78卷 408-413页

作者： Lin, Shao-Bin Xie, Ying-Jun Chen, Zheng Zhou, Yi Wu, Jian-Zhu Zhang, Zhi-Qiang Shi, Shan-Shan Chen, Bao-Jiang Fang, Qun Sun Yat Sen Univ Fetal Med Ctr Dept Obstet & Gynecol Affiliated Hosp 1 Guangzhou 510080 Guangdong Peoples R China Sun Yat Sen Univ Dept Med Genet Zhongshan Med Coll Guangzhou 510080 Guangdong Peoples R China Jinan Univ Dept Fetal Med Ctr Affiliated Hosp 1 Guangzhou Guangdong Peoples R China

Background: Conventional karyotyping has been a routine method to identify chromosome abnormalities in products of conception. However, this process is being transformed by single nucleotide polymorphism (SNP) array, which has advantages over karyotyping, including higher resolution and dispensing with cell culture. Therefore, the purpose of this study was to evaluate the advantage of high-resolution SNP array in identifying genetic aberrations in products of conception. Methods: We consecutively collected 155 products of conception specimens, including 139 from first-trimester miscarriage and 16 from second-trimester miscarriage. SNP array was performed on these samples in parallel with G-banded karyotyping. Results: The test success rate was 98.1% (152/155) using SNP array, which was higher than that using karyotyping (133/155, 85.8%). It yielded a 63.8% (97/152) abnormality rate, and the frequency of various chromosome abnormalities was in agreement with other previous studies. The results between array and karyotyping demonstrated a 94.0% (125/133) concordance. SNP array obtained additional aberrations in 3.8% (5/133) of those cases unidentified by karyotyping, which included three cases with whole-genome uniparental disomy, one with pathogenic copy number variation, and one with del(4)(q35.1q35.2) and dup(12)(q24.31q24.33). However, chromosome translocations presented in two cases and tetraploidy presented in one case were detected by karyotyping instead of array. Additionally, two out of three cases with mosaic trisomy were revealed by array but recognized as pure trisomy by karyotyping. Conclusion: This study demonstrated that SNP array had certain advantages over G-banded karyotyping, including a higher success rate, additional detection of copy number variations and uniparental disomy, and improved sensitivity to mosaicism. Therefore, it would be an alternative method to karyotyping in clinical genetic practice. Copyright (C) 2015 Elsevier Taiwan LLC and th

关键词： copy number variation karyotyping products of conception single nucleotide polymorphism array uniparental disomy

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An extragonadal yolk sac tumor presumed to be of postmeiotic germ cell origin by genetic zygosity analysis via single nucleotide polymorphism array

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GENES CHROMOSOMES & CANCER 2020年第3期59卷 209-213页

作者： Tamura, Daisuke Maeda, Daichi Sato, Toshiharu Sugawara, Tae Shirasawa, Hiromitsu Shimizu, Dai Sato, Naoki Goto, Akiteru Terada, Yukihiro Akita Univ Grad Sch Med Dept Obstet & Gynecol 1-1-1 Hondo Akita Akita 0108543 Japan Akita Red Cross Hosp Dept Gynecol Akita Japan Osaka Univ Grad Sch Med Dept Clin Genom Osaka Japan Akita Univ Grad Sch Med Dept Cellular & Organ Pathol Akita Japan

An extragonadal yolk sac tumor (YST) is a rare malignant germ cell tumor that usually occurs in childhood. The pathogenesis of extragonadal YST remains largely unknown, especially with regards to its cell of origin. Herein, we report a case of extragonadal YST arising in the uterine round ligament. A 31-year-old Japanese woman, para 2, underwent partial resection of a left-sided, 5-cm, solid inguinal mass. Intraoperative findings showed enlargement of the uterine round ligament in the inguinal canal. Pathological evaluation diagnosed the mass as YST with a mature teratoma (MT) component. The preoperative alpha-fetoprotein level was markedly elevated, at 24 790 ng/mL. Postoperative magnetic resonance imaging revealed a right ovarian MT and a 3-cm mass remaining in the left lower abdominal wall. The patient underwent total abdominal hysterectomy, bilateral adnexectomy, and left inguinal mass resection. We sampled three frozen tissues (YST, right ovarian MT, and left normal ovary) and performed a single nucleotide polymorphism (SNP) array. Pathological evaluation revealed remnant extragonadal YST in the left inguinal region. The SNP array demonstrated a completely homozygous YST genotype. Copy number variations were gains of 1p, 1q, 2p, 3p, 7p, 8p, 10q, 14q, 18p, 20q, Xp, and Xq and losses of 12q, 20p, and Xq. The right ovarian MT and left normal ovary were partially homozygous and heterozygous, respectively. The evidence suggests that this neoplasm is presumed to be a postmeiotic germ cell origin.

关键词： extragonadal germ cell tumor genetic zygosity single nucleotide polymorphism array yolk sac tumor

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Genome-wide analysis of loss of heterozygosity and copy number amplification in uterine leiomyomas using the 100K single nucleotide polymorphism array

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EXPERIMENTAL AND MOLECULAR PATHOLOGY 2011年第1期91卷 434-439页

作者： Meadows, Kellen L. Andrews, Danica M. K. Xu, Zongli Carswell, Gleta K. Laughlin, Shannon K. Baird, Donna D. Taylor, Jack A. Natl Inst Environm Hlth Sci Mol Carcinogenesis Lab Res Triangle Pk NC 27709 USA Natl Inst Environm Hlth Sci Microarray Grp Res Triangle Pk NC 27709 USA Natl Inst Environm Hlth Sci Epidemiol Branch Res Triangle Pk NC 27709 USA

Purpose: Uterine leiomyomas (fibroids) are benign smooth muscle tumors commonly found among reproductive-aged women. Though benign, these tumors are the leading indication for hysterectomies in the United States and cause significant morbidity. Despite the importance of this tumor in women's health, relatively little is known about the molecular etiology. Methods: In this study, we used the Affymetrix 100K single nucleotide polymorphism (SNP) chip to assess whether the pattern and frequency of genome-wide loss of heterozygosity (LOH) and copy number amplifications is associated with clinical heterogeneity. Results: Thirty-seven tumors with varying sizes and histology from eleven patients were analyzed. LOH was observed in 4/37 tumors (10.8%) and significantly associated with large-sized tumors (p<0.0014). Two tumors revealed hemizygosity on chromosome 7q, a region that has been consistently reported to have LOH. Additionally, we detected one novel region of LOH, 16p13.11 in one tumor (2.7%). Copy number amplifications were observed on all chromosomes;however, most were low-level amplifications and only detected in a single tumor. One region of amplification at 3p26.3 was detected in four tumors. Conclusions: Despite the use of a high-density SNP platform, our results suggest that genome-wide LOH and copy number amplifications are infrequent events and generally do not determine clinical and histologic characteristics of this disease. Published by Elsevier Inc.

关键词： Uterine leiomyoma single nucleotide polymorphism array LOH Copy number amplification

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The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes

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BRITISH JOURNAL OF HAEMATOLOGY 2016年第2期174卷 292-301页

作者： Olsson, Linda Zettermark, Sofia Biloglav, Andrea Castor, Anders Behrendtz, Mikael Forestier, Erik Paulsson, Kajsa Johansson, Bertil Lund Univ Div Clin Genet Dept Lab Med Lund Sweden Dept Clin Genet Div Lab Med Off Med Serv Lund Sweden Skane Univ Hosp Dept Paediat Lund Sweden Linkoping Univ Hosp Dept Paediat Linkoping Sweden Umea Univ Dept Med Biosci Umea Sweden

Cytogenetic analyses of a consecutive series of 67 paediatric (median age 8 years;range 0-17) de novo acute myeloid leukaemia (AML) patients revealed aberrations in 55 (82%) cases. The most common subgroups were KMT2A rearrangement (29%), normal karyotype (15%), RUNX1-RUNX1T1 (10%), deletions of 5q, 7q and/or 17p (9%), myeloid leukaemia associated with Down syndrome (7%), PML-RARA (7%) and CBFBMYH11 (5%). single nucleotide polymorphism array (SNP-A) analysis and exon sequencing of 100 genes, performed in 52 and 40 cases, respectively (39 overlapping), revealed >= 1 aberration in 89%;when adding cytogenetic data, this frequency increased to 98%. Uniparental isodisomies (UPIDs) were detected in 13% and copy number aberrations (CNAs) in 63% (median 2/case);three UPIDs and 22 CNAs were recurrent. Twenty-two genes were targeted by focal CNAs, including AEBP2 and PHF6 deletions and genes involved in AML-associated gene fusions. Deep sequencing identified mutations in 65% of cases (median 1/case). In total, 60 mutations were found in 30 genes, primarily those encoding signalling proteins (47%), transcription factors (25%), or epigenetic modifiers (13%). Twelve genes (BCOR, CEBPA, FLT3, GATA1, KIT, KRAS, NOTCH1, NPM1, NRAS, PTPN11, SMC3 and TP53) were recurrently mutated. We conclude that SNP-A and deep sequencing analyses complement the cytogenetic diagnosis of paediatric AML.

关键词： paediatric acute myeloid leukaemia single nucleotide polymorphism array targeted deep exon sequencing

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