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%.
CONCLUSIONS: 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.

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.
CONCLUSIONS: Through combined cytogenetic and molecular genetic analysis, a sSMC derived from chromosome 9 was delineated, which has enabled genetic counseling for the couple.

Evidence suggests that the pericentric inversion of chromosome 9 (inv(9)) does not affect the aneuploidy rate (38.5%) after IVF. Herein, we report a successful live female twin birth through IVF/ICSI with a high aneuploidy rate from a couple within which the infertile father has inv(9)(p12q13). A couple (a 34-year-old male and a 35-year-old female) was referred to our clinic due to infertility. The wife has a child with her previous husband. Results from the infertility workup of both parents were normal. Karyotyping revealed that the inv(9)(p12q13) of the father was the only cytogenetic abnormality. Preimplantation genetic testing for aneuploidies (PGT-A) after IVF/ICSI revealed a high aneuploidy rate (77%; 10/13). Two euploid blastocysts were transferred, resulting in a successful live female twin birth. The presented case highlights the possibility that inv(9)(p12q13) in males may impact the fertility and euploidy rate. PGT-A facilitates the selection of qualified blastocysts for the optimization of live-birth outcomes.

BACKGROUND: Hydrocephalus caused by excessive liquor production due to choroid plexus hyperplasia is a rare condition that may necessitate unusual treatment paradigms. It can be seen in trisomy 9p where coexisting congenital heart disease additionally may complicate the therapeutic approach as illustrated in the current case report.
METHODS: At 20 months of age, a Caucasian girl with trisomy 9 and family history of an older brother and twin sister having the same syndrome displayed sign of congenital hydrocephalus due to increasing head circumference. Magnetic resonance imaging revealed enlarged lateral ventricles and a prominent choroid plexus, and the girl was treated with a ventriculoperitoneal shunt, which 2 days later had to be replaced with a ventriculoatrial shunt as cerebrospinal fluid formation greatly exceeded the ability of the patient\'s abdominal absorptive capability. At 16 years of age, the patient was diagnosed with cardiomyopathy and diminished ejection fraction. Some months later, she was admitted to the neurosurgical ward showing signs of shunt dysfunction due to a colloid cyst in the third ventricle. Cystic drainage through endoscopic puncture only helped temporarily. Revision of the shunt system showed occlusion of the ventricular drain, and replacement was merely temporary alleviating. Intracerebral pressure was significantly increased at around 30 mmHg, prompting externalization of the drain, and measurements revealed high cerebrospinal fluid production of 60-100 ml liquor per hour. Thus, endoscopic choroid plexus coagulation was performed bilaterally leading to an immediate decrease of daily cerebrospinal fluid formation to 20-30 ml liquor per hour, and these values where stabilized by pharmaceutical treatment with acetazolamide 100 mg/kg/day and furosemide 1 mg/kg/day. Subsequently a ventriculoperitoneal shunt was placed. Follow-up after 1 and 2 months displayed no signs of hydrocephalus or ascites.
CONCLUSIONS: High cerebrospinal fluid volume load and coexisting heart disease in children with trisomy 9p may call for endoscopic choroid plexus coagulation and pharmacological therapy to diminish the daily cerebrospinal fluid production to volumes that allow proper ventriculoperitoneal shunting.

Tetrasomy 9p is a rare genetic condition which usually results from a supernumerary isochromosome derived from the short arm of chromosome 9. Phenotypic findings include multiple congenital anomalies, facial dysmorphism, growth and developmental delays, and also vary according to the presence and degree of mosaicism.
We report on a newborn with tetrasomy 9p who deceased in the newborn period. She had facial features including low-set and anteverted ears, hypertelorism, prominent nasal bridge, and microretrognathia. Bilateral ventriculomegaly, vermian hypoplasia and corpus callosum agenesis were detected on magnetic resonance imaging and double outlet right ventricle (tetralogy of Fallot type), secundum atrial septal defect, and persistent left superior vena cava were displayed by echocardiography. Microarray analysis revealed 38,584 kb tetrasomic region at 9p24.3p13.1. We also present a review of the literature suggesting that there is a recognizable phenotype for this condition and an assessment of cardiac manifestations based on the size and the localization of the breakpoints.
We conclude that cardiac manifestations do not differ according to the localization of the breakpoint. Persistent left superior vena cava seems to be consistent with breakpoints distal to q12, but the present case is different from them by breakpoint p13.1.

OBJECTIVE: Tetrasomy 9p is a rare fetal condition. Cases are usually mosaic. Here, we present a non-mosaic tetrasomy 9p case with cytogenetic analysis, fluorescence in situ hybridization, microarray data, ultrasound findings, and phenotypic presentation.
METHODS: A pregnancy was referred to cytogenetic analysis because of increased nuchal translucency in prenatal ultrasound at 13 weeks of gestation. Prenatal laboratory analysis revealed an extra marker chromosome with a non-mosaic pattern. Ultrasonographic findings were unilateral cleft lip and palate, micrognathia, and atrioventricular septal defect at the 17th week; additionally, ventriculomegaly, left axis deviation of the fetal heart, and a single umbilical artery were determined at the 23rd week.
CONCLUSIONS: Phenotypic severity in non-mosaic tetrasomy 9p widely differs depending on the chromosomal content. We recommend performing appropriate genetic tests in those pregnancies with the suspicion of tetrasomy 9p, evaluating the mosaic state, and following those cases with detailed ultrasonographic examinations.

There are an estimated > 400 million people living with a rare disease globally, with genetic variants the cause of approximately 80% of cases. Next Generation Sequencing (NGS) rapidly identifies genetic variants however they are often of unknown significance. Low throughput functional validation in specialist laboratories is the current ad hoc approach for functional validation of genetic variants, which creating major bottlenecks in patient diagnosis. This study investigates the application of CRISPR gene editing followed by genome wide transcriptomic profiling to facilitate patient diagnosis. As proof-of-concept, we introduced a variant in the Euchromatin histone methyl transferase (EHMT1) gene into HEK293T cells. We identified changes in the regulation of the cell cycle, neural gene expression and suppression of gene expression changes on chromosome 19 and chromosome X, that are in keeping with Kleefstra syndrome clinical phenotype and/or provide insight into disease mechanism. This study demonstrates the utility of genome editing followed by functional readouts to rapidly and systematically validating the function of variants of unknown significance in patients suffering from rare diseases.

Inversion of chromosome 9 (inv[9]) is known as one of the most common structural balanced chromosomal variations. Chromosome 9 is highly susceptible to structural rearrangements, specifically to pericentric inversions. Various investigators have posited that inv(9) with different breakpoints could be the cause of several abnormal conditions in individuals, whereas others have considered it a benign variant. To our knowledge, a consensus regarding the effects of this inversion has yet to emerge.
This study aims to discuss the pathogenic/benign effects of inv(9) in all possible clinical conditions detected in the occurrence of this abnormality.
Studies on inv(9) were collected via PubMed, MalaCards, Google Scholar, and NORD, along with the search terms of inv(9), pericentric inv(9), and chromosome 9 variants. Additionally, the incidence of inv(9) and the karyotype and clinical findings of individuals reported with this variant were investigated.
The collection of the studies reviewed shows that inv(9) is associated with various conditions such as congenital anomalies, growth retardation, infertility, recurrent pregnancy loss, and cancer. The clinical features associated with this variant in humans vary between growth stages. Further, there have been no shared clinical findings in a specific period.
Although there is no conclusive evidence for the pathogenicity of this rearrangement, prenatal genetic counseling on inv(9) and further clinical and molecular studies would be helpful in chromosome 9-related problems.

Kleefstra syndrome (KS) is a genetic syndrome caused by a haploinsufficiency of the EHMT1 gene and characterized by intellectual disability, language disorders, childhood hypotonia and distinct facial features. Only a few cases of first episode of psychosis in KS have already been reported. We describe a young female patient with KS who presented a first episode of psychosis. In a context of an initial diagnosis wavering and a lack of recommendations, this clinical observation illustrates the importance of psychiatric comorbidities and their diagnostic and therapeutic complexity in KS; with a need for multidisciplinary management considering its specific aspects and vulnerabilities.

Tetrasomy 9p (ORPHA:3390) is a rare syndrome, hallmarked by growth retardation; psychomotor delay; mild to moderate intellectual disability; and a spectrum of skeletal, cardiac, renal and urogenital defects. Here we present a Chinese female with good past health who conceived her pregnancy naturally. Non-invasive prenatal testing (NIPT) showed multiple chromosomal aberrations were consistently detected in two sampling times, which included elevation in DNA from chromosome 9p. Amniocentesis was performed and sent for chromosomal microarray, which was normal. Maternal karyotype revealed that mos 47,XX,+dic(9;9)(q21.1;q21.1)(24)/46,XX(9) presents mosaic tetrasomy for the short arm of chromosome 9p and is related to the NIPT results showing elevation in DNA from chromosome 9p. The pregnancy was uneventful, and the patient was delivered at term. Maternal samples were obtained at two different time points after delivery showed the same multiple chromosomal aberrations detected during pregnancy. This is a first report on an unusual case of mosaic isodicentric tetrasomy 9p in a healthy adult with normal intellect. With widespread adoption of NIPT for screening fetal aneuploidy and genome-wide copy number changes, a rise in incidental detection of maternal rare genetic syndrome will bring challenges in our current approach to genetic counselling and prenatal diagnosis.