OBJECTIVE: To explore the genetic basis for a rare case of acute B-lymphocytic leukemia (B-ALL) with double Philadelphia chromosomes (Ph) and double derivative chromosome 9s [der(9)]. METHODS: A patient with double Ph and double der(9) B-ALL who presented at Shanghai Zhaxin Intergrated Traditional Chinese and Western Medicine Hospital in June 2020 was selected as the subject. Bone marrow morphology, flow cytometry, G-banding karyotyping, fluorescence in situ hybridization (FISH), genetic testing and chromosomal microarray analysis (CMA) were used to analyze bone marrow samples from the patient at various stages. RESULTS: At initial diagnosis, the patient's bone marrow morphology and flow immunotyping have both supported the diagnosis of B-ALL. G-banded karyotyping of the patient indicated double Ph, in addition with hyperdiploid chromosomes involving translocations between chromosomes 9 and 22. BCR-ABL1 fusion gene was positive. Genetic testing at the time of recurrence revealed presence of a heterozyous c.944C>T variant in the kinase region of the ABL1 gene. FISH showed a signal for ABL1-BCR fusion on both chromosome 9s. CMA showed that the mosaicism homozygosity ratio of chromosome 9 was about 40%, and the mosaicism duplication ratio of chromosome 22 was about 43%. CONCLUSION Since both der(9) homologs were seen in 40% of cells, the possible mechanism for the double der(9) in this patient may be similar to that of double Ph, which might have resulted from non-disjunction during mitosis in the Ph chromosome-positive cell clone.
Humans ; Philadelphia Chromosome ; In Situ Hybridization, Fluorescence/methods* ; China ; Chromosome Aberrations ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics* ; Translocation, Genetic ; Fusion Proteins, bcr-abl/genetics* ; Chromosomes, Human, Pair 9/genetics*

OBJECTIVE: To explore the genetic basis of three children with unexplained developmental delay/intellectual disability (DD/ID). METHODS: Peripheral blood samples were collected from the patients and subjected to chromosomal microarray analysis (CMA). RESULTS: Patient 1 was found to harbor a 190 kb deletion at 9q34.3, which encompassed most of EHMT1 (OMIM 607001), the key gene for Kleefstra syndrome (OMIM 610253). Patients 2 and 3 were siblings. CMA showed that they have shared four chromosomal copy number variations (CNVs) including a deletion at 9q34.3 which spanned 154 kb and 149 kb, respectively, and encompassed the EHMT1 and CACNA1B (OMIM 601012) genes. The remaining 3 CNVs were predicted to be with no clinical significance. CONCLUSION Microdeletions at 9q33.4 probably underlay the pathogenesis of DD/ID in the three children, for which EHMT1 may be the key gene.
Child ; Chromosome Deletion ; Chromosomes, Human, Pair 9 ; Craniofacial Abnormalities/genetics* ; DNA Copy Number Variations ; Developmental Disabilities/genetics* ; Heart Defects, Congenital ; Humans ; Intellectual Disability/genetics*

OBJECTIVE: To delineate a small supernumerary marker chromosome (sSMC) derived from chromosome 9 with combined cytogenetic and molecular methods. METHODS: For a pregnant woman with fetal ultrasound revealing left ventricular punctate hyperechoic echo, and a high risk for monosomy or partial deletion of chromosome 8, chromosome 9 trisomy, monosomy or partial deletion of chromosome 11 by non-invasive prenatal testing, and an abnormal MOM value revealed by mid-term serum screening, amniocentesis was performed for G banded chromosomal analysis and single nucleotide polymorphism array (SNP-array) assay. Peripheral blood samples of the woman and her spouse were also collected for the above tests. In addition, the woman was further subjected to C banding karyotyping analysis and fluorescence in situ hybridization (FISH) assay. RESULTS: The G-banded karyotype of the pregnant women was 47,XX,+mar[20]/46,XX[80], whilst C-banding analysis showed a deep stain in the middle of the sSMC (suggestive of centromeric region) and light stain at both ends (suggestive of euchromatism). FISH combined with DAPI banding analysis using 9pter/9qter probes revealed a karyotype of 47,XX,+mar.ish i(9)(9p10)(9p++)[2]/46,XX[18], whilst SNP-array has revealed a 68.1 Mb duplication in the 9p24.3q13 region. A database search has suggested the duplication to be likely pathogenic. No abnormality was found in her fetus and spouse by karyotyping and SNP-array analysis. CONCLUSION Through combined cytogenetic and molecular genetic analysis, a sSMC derived from chromosome 9 was delineated, which has enabled genetic counseling for the couple.
Female ; Humans ; Pregnancy ; Biomarkers ; Chromosomes, Human, Pair 9/genetics* ; Genetic Testing ; In Situ Hybridization, Fluorescence ; Monosomy

OBJECTIVE: To analyze the clinical and genetic features of three patient diagnosed with Kleefstra syndrome. METHODS: Whole exome sequencing (WES) was carried out for the probands and their parents. Suspected variants were validated by Sanger sequencing. Copy number variations (CNV) were detected by CNV-seq and validated by real-time PCR. RESULTS: Proband 1 was found to carry a de novo heterogeneous variant (c.823+1G>T) of the EHMT1 gene, which may affect its expression. Based on the guidelines of the American College of Medical Genetics and Genomics, the variant was predicted to be pathogenic (PVS1+PS2+PM2). Proband 2 was found to carry a de novo missense variant c.439C>G (p.L147V) of the EHMT1 gene, which was predicted to be likely pathogenic (PS2+PM1+PM2+PP3). Proband 3 was found to carry a heterozygous 520 kb deletion at 9q34.3 by CNV-seq. The deletion has encompassed the whole of the EHMT1 gene. Real-time PCR has detected no CNV of this region in her parents. CONCLUSION Variants of the EHMT1 gene probably underlay the disease in these patients. Genetic testing has provided a basis for their clinical diagnosis.
Chromosome Deletion ; Chromosomes, Human, Pair 9 ; Craniofacial Abnormalities ; DNA Copy Number Variations ; Female ; Genetic Testing ; Heart Defects, Congenital ; Humans ; Intellectual Disability/genetics* ; Mutation

OBJECTIVE: To perform prenatal diagnosis, pedigree analysis, and genetic counseling of a pregnant woman who gave birth to a child with Kleefstra syndrome. METHODS: Karyotype analysis, chromosomal microarray analysis (CMA), multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) were used of peripheral blood and amniotic fluid to find causes. Recurrence risk assessment was performed later. RESULTS: The amniotic fluid sample showed a 9q34.3 microduplication of arr (hg19) 9q34.3 (140 168 806-141 020 389)× 3, which overlapped the 9q34.3 microdeletion region of proband. The pregnant woman was detected with a balanced translocation of ish, t(9;17)(9q34.3; qter) (9p+; 17p+,9q+, 17q+). No other abnormal results were found in the family. CONCLUSION Offspring who share the same chromosome segment deletion or duplication are always from parent who carries balanced chromosomal structural aberration.
Chromosome Aberrations ; Chromosome Deletion ; Chromosomes, Human, Pair 9/genetics* ; Female ; Genetic Testing ; Humans ; In Situ Hybridization, Fluorescence ; Pregnancy

OBJECTIVE: To determine the nature and origin of aberrant chromosomes in a child with multiple anomalies and psychomotor retardation. METHODS: Routine G-banding was carried out to analyze the karyotypes of the patient and his parents, and next generation sequencing for copy number variations (CNV-seq) was used for the fine mapping of the aberrant chromosomal regions. RESULTS: The proband and his uncle exhibited psychomotor retardation, craniofacial malformation, infantile external genitalia, and concealed penis. Cytogenetic analysis indicated that the child has a 46,XYqh+,+(9),t(9;13)(q13;q12),pat,-13 karyotype. His uncle was XYqh+,+(9),t(9;13)(q13;q12)mat,-13, his father was 46,XYqh+,t(9;13)(q13;q12)mat, his grandmother was 46,XX,t(9;13)(q13;q12), and his grandfather was 46,XYqh+. The result of CNV-seq assay for the child was 46,XY,+9p(pter-p13.2,-40 Mb×3). No deletion was detected. CONCLUSION The partial trisomy 9 and partial monosomy 13 probably underlie the phenotypic abnormalities in the child. Combined chromosomal karyotyping and DNA sequencing can facilitate delineation of the nature and origin of the aberrant chromosomes.
Abnormalities, Multiple ; Child ; Chromosome Deletion ; Chromosomes, Human, Pair 13 ; Chromosomes, Human, Pair 9 ; DNA Copy Number Variations ; Humans ; Karyotyping ; Male ; Monosomy ; Pedigree ; Translocation, Genetic ; Trisomy

OBJECTIVE: To analyze the clinical and molecular genetic characteristics of patient with Kleefstra syndrome 1. METHODS: Clinical data, chromosomal karyotype and whole genome copy number variations (CNVs) of the patient were analyzed. RESULTS: The patient was found to have a karyotype of 45,XX,-9[4]/46,XX,r(9)(p24q34)[56]. Whole-genome CNVs detection revealed that she has carried a heterozygous deletion of approximately 670 kb at 9q34.3, which encompassed the entire EHMT1 gene. The region is strongly associated with Kleefstra syndrome (1/9q telomere deletion). In addition, the patient also had heterozygous deletion of 9pter, which may predispose to formation of ring chromosome 9. CONCLUSION The child was diagnosed with Kleefstra syndrome type 1 in conjunct with ring chromosome 9.
Child ; Chromosome Deletion ; Chromosomes, Human, Pair 9 ; genetics ; Craniofacial Abnormalities ; genetics ; DNA Copy Number Variations ; Female ; Heart Defects, Congenital ; genetics ; Humans ; Intellectual Disability ; genetics ; Ring Chromosomes

BACKGROUND: To analyze the frequency of atypical fluorescence in situ hybridization signal patterns and estimate the complete cytogenetic response (CCyR) and major molecular response (MMR) during 12 months of tyrosine kinase inhibitor therapy in patients with newly diagnosed chronic myeloid leukemia. METHODS: The study included bone marrow and peripheral blood samples from 122 patients with newly diagnosed chronic myeloid leukemia. Detection of the breakpoint cluster region—Abelson fusion gene (BCR-ABL1) was performed using fluorescence in situ hybridization with a dual-color dual-fusion translocation probe, and MMR analysis was performed using the real-time quantitative polymerase chain reaction method. RESULTS: Variant translocation was determined in 10 samples and a deletion on the derivative chromosome 9 (del/der(9)) was found in 20 samples. The rates of CCyR and MMR were similar between patients with reciprocal translocation, variant translocation, deletion of derivative BCR, or ABL1-BCR fusion gene. The Kaplan-Meier test did not show any significant differences in the rates of CCyR and MMR among those groups of patients. CONCLUSION: The frequencies of variant translocation and del/der(9) in the present study agree with the results of other studies performed worldwide. No differences were observed in the rates of CCyR and MMR between patients with atypical patterns and reciprocal translocation.
Bone Marrow ; Chromosomes, Human, Pair 9 ; Cytogenetics ; Fluorescence ; Humans ; In Situ Hybridization ; Incidence* ; Kaplan-Meier Estimate ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive* ; Leukemia, Myeloid ; Methods ; Polymerase Chain Reaction ; Protein-Tyrosine Kinases* ; Tyrosine*

OBJECTIVE: To explore the genetic cause for a child featuring growth and mental retardation. METHODS: Following conventional karyotyping analysis of the trio family, next generation sequencing (NGS) was carried out to explore the origin of the supernumerary marker chromosome. Fluorescence in situ hybridization (FISH) was used to confirm the result. RESULTS: The karyotypes of both parents were normal, while the proband was found to be 47,XX,+mar. NGS showed that the supernumerary marker has originated from chromosome 9p13.1p24.3 with a size of 39.77 Mb. FISH has confirmed the above finding. CONCLUSION The 9p13.1-p24.3 trisomy probably underlies the abnormal phenotypes of the child. Cytogenetic analysis combined with NGS and FISH can provide accurate diagnosis for such disorders.
Child ; Chromosomes, Human, Pair 9 ; genetics ; Cytogenetic Analysis ; High-Throughput Nucleotide Sequencing ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Trisomy

We present a case of a 71-year-old male Chamorro patient from Guam who presented with progressive supranuclear palsy (PSP)-Richardson’s syndrome. Considering his strong family history of parkinsonism and a PSP phenotype, he was clinically diagnosed with Guam parkinsonism-dementia complex (PDC). Magnetic resonance imaging (MRI) of the brain revealed prominent midbrain atrophy with preserved pontine volume, forming the ‘hummingbird’ sign, which has not been described before in Guam PDC. Molecular analysis of the chromosome 9 open reading frame 72 gene (C9orf72) showed only 6 GGGGCC repeats. We discuss the clinico-pathological similarities and differences between PSP and Guam PDC, and highlight the topography of neuropathological changes seen in Guam PDC to explain the appearance of the ‘hummingbird’ sign on MRI.
Aged ; Atrophy ; Brain ; Chromosomes, Human, Pair 9 ; Guam* ; Humans ; Magnetic Resonance Imaging ; Male ; Mesencephalon ; Open Reading Frames ; Parkinsonian Disorders ; Phenotype ; Supranuclear Palsy, Progressive