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Case Studies


T-cell acute lymphoblastic leukemia (T-ALL) is characterized by translocations of oncogenic transcription factor genes and T-cell receptor loci. This study reported the first case of T-ALL with TCR alpha/delta (TRA/D) locus rearrangements associated with t(11;14)(p13;q11.2), inv(14)(q11.2q32), and clonal evolution of JAK2 rearrangement. Our JAK2 break-apart probe was used to detect a novel JAK2 translocation, t(8;9)(p22;p24), in the subject under study. As the patient tested negative for JAK2 rearrangements at diagnosis, the translocation must have developed during disease progression.

Published: 08/19/2019

Related Probes: JAK2 Break Apart Fish Probe


CNTN4 copy number variations (CNVs) have been reported in children with autism spectrum disorder (ASD) and other neurodevelopmental conditions. In this study, three unrelated patients with CNTN4 CNVs were genetically and clinically characterized. Empire Genomics’ RP11-51F24 FISH probe helped to confirm CNTN4 loss in a patient with deletion of the gene. Results both point to CNTN4 as a potential regulator of language development, and call for further evaluation of affected individuals via comprehensive phenotyping to better understand the mechanisms of reduced penetrance and variable expressivity of CNTN4 CNVs.

Published: 08/15/2019

Related Probes: RP11-51F24 Fish Probe


The subject of this study was a 17 month old girl who had prenatal intrauterine growth restriction and cardiac defects. She was found to have inverted duplication of 3p with an adjacent terminal 3p deletion, revealed by microarray analysis and FISH. Empire Genomics’ RP11-451A20 FISH probe was used to confirm duplication and rearrangement of 3p. Only one postnatal patient and one second trimester pregnancy have been reported with this finding. Many of her features were shared with both previously reported patients, including congenital heart disease, growth restriction, microcephaly, hypotonia, and developmental delay. However, the subject also had additional features not reported in cases of 3p deletion or duplication, such as aortic dilation, hemangiomas, and neutropenia.

Published: 07/25/2019

Related Probes: RP11-451A20 Fish Probe


The subject of this study was a two-and-a-half-year-old patient with an extensive list of developmental and physical abnormalities (e.g. trouble feeding, dysmorphic facial features, severe language delays). FISH analysis was performed on the patient to investigate potential genetic causes of her condition. Empire Genomics’ RP11-227H15 FISH probe was used to detect a de novo 10.2 MB deletion extending from 10q21.3-10q22.3, the second largest reported deletion in this region. Based on the patient’s unique clinical presentation, the team concluded that loss of the KAT6B was the likeliest cause of her condition.

Published: 05/17/2019

Related Probes: RP11-227H15 Fish Probe


Interstitial deletions of chromosome 9q, although rare, are characteristic of many congenital abnormalities, including dysmorphic features, developmental delay, and intellectual disability. A child with global developmental delay (GDD) and a de novo interstitial 7.0 Mb deletion of 9q21.33/q22.31 was studied. The deletion was confirmed using a BAC FISH probe (RP11-91M3) from Empire Genomics. The patient was unique in that her condition was less severe than the majority of 9q deletion cases, suggesting that her “…clinical synopsis is not predicted simply by the roles of each of the genes involved in this novel interstitial deletion.”

Published: 05/07/2019

Related Probes: RP-11 91M3 Fish Probe


The subject of this study was a 3 year-old male, born to nonconsanguineous healthy parents, who presented with various physical and developmental abnormalities. The toddler was found to have the first reported balanced chromosomal complex rearrangement involving chromosomes 1, 9 and 10, inherited from his partially affected mother. FISH probes from Empire Genomics verified the 1qter and 10qter rearrangement after microarray analysis.

Published: 04/02/2019

Related Probes: RP11-108K14 Fish Probe


Autism is a common developmental disorder that has increased substantially in frequency since the 2000s. Studies have looked into various factors (vitamin deficiencies, viral infections, parental age) as potential causes of the condition, but no clear relationship has been found. In the last decade, studies have started to focus more on possible genetic causes. This study did just that, investigating a duplication on chromosome Xq13.1 in a patient with autism. Empire Genomics’ NLGN3 FISH probe helped to confirm the duplication.

Published: 01/31/2019

Related Probes: NLGN3 Fish Probe


The MYCN-IGH fusion has been described in blastic mantle cell lymphoma and follicular lymphoma, but, at the time of this study, still hadn’t been identified in marginal zone B-cell lymphoma (MZL). This study presented the first documented case of MYCN-IGH fusion in a MZL patient. Cytogenetic testing, including FISH, was performed to analyze the patient’s genome. Our CCND2 break apart probe and RP11-542H15 BAC FISH probe were used to detect CCND2 and MYCN rearrangements.

Published: 01/31/2019

Related Probes: RP11-542H15 Fish Probe


Mutations in voltage-gated sodium channel (SCN) genes are thought to contribute to the development of certain psychiatric and neurological diseases. The subject of this study was a 28 year old male with autism and Tourette syndrome, who was found to have a heterozygous 718 kb deletion at 2q24.3, leading to loss of 2 SCN genes (SCN2A and SCN3A), as well as GRB14, COBBL1, and SCL38A11. Empire Genomics’ RP11-150F4 FISH probe confirmed deletion of SCN2A.

Published: 07/31/2018

Related Probes: RP11-150F4 Fish Probe


Our ETV6-NTRK3 fusion probe was used to detect fusion of the two genes in a 36 year old patient with a neck tumor originally diagnosed as papillary thyroid carcinoma. After thyroid-targeted treatment proved unsuccessful, further cytogenetic analysis revealed the presence of a NTRK3-ETV6 fusion consistent with MASC’s clinical profile.

Published: 04/13/2016

Related Probes: ETV6-NTRK3 Fish Probe