Publication in Clinical Cancer Research

Clin Cancer Res. 2018 Dec 26. pii: clincanres.3230.2018. doi: 10.1158/1078-0432.CCR-18-3230. [Epub ahead of print]

Epigenetic silencing of miRNA-338-5p and miRNA-421 drives SPINK1-positive prostate cancer.

Bhatia V1, Yadav A1, Tiwari R1, Nigam S1, Goel S1, Carskadon S2, Gupta N3, Goel A4, Palanisamy N5, Ateeq B6.

Author information

1

Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur.

2

Henry Ford Health System.

3

Pathology, Henry Ford Health System.

4

Department of Urology,, King George's Medical University.

5

Urology, Henry Ford Health System.

6

Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur bushra@iitk.ac.in.

Abstract

PURPOSE:

Serine Peptidase Inhibitor, Kazal type-1 (SPINK1) overexpression defines the second most recurrent and aggressive prostate cancer (PCa) subtype. However, the underlying molecular mechanism and pathobiology of SPINK1 in PCa remains largely unknown.

EXPERIMENTAL DESIGN:

MicroRNA-prediction tools were employed to examine the SPINK1-3'UTR for miRNAs binding. Luciferase reporter assays were performed to confirm the SPINK1-3'UTR binding of shortlisted miR-338-5p/miR-421. Further, miR-338-5p/-421 overexpressing cancer cells (SPINK1-positive) were evaluated for oncogenic properties using cell-based functional assays and mice xenograft model. Global gene expression profiling was performed to unravel the biological pathways altered by miR-338-5p/-421. Immunohistochemistry and RNA in-situ hybridization was carried-out on PCa patients' tissue microarray for SPINK1 and EZH2 expression respectively. Chromatin immunoprecipitation assay was performed to examine EZH2 occupancy on the miR-338-5p/-421 regulatory regions. Bisulfite sequencing and methylated DNA-immunoprecipitation was performed on PCa cell lines and patients' specimens.

RESULTS:

We established a critical role of miRNA-338-5p/-421 in post-transcriptional regulation of SPINK1. Ectopic expression of miRNA-338-5p/-421 in SPINK1-positive cells abrogate oncogenic properties including cell-cycle progression, stemness and drug resistance, and show reduced tumor burden and distant metastases in mice model. Importantly, we show SPINK1-positive PCa patients exhibit increased EZH2 expression, suggesting its role in epigenetic silencing of miRNA-338-5p/-421. Furthermore, presence of CpG dinucleotide DNA methylation marks on the regulatory regions of miR-338-5p/-421 in SPINK1-positive PCa cells and patients' specimens confirms epigenetic silencing.

CONCLUSION:

Our findings revealed that miRNA-338-5p/-421 are epigenetically silenced in SPINK1-positive PCa, while restoring the expression of these miRNAs using epigenetic drugs or synthetic mimics could abrogate SPINK1-mediated oncogenesis.

Copyright ©2018, American Association for Cancer Research.

PMID:

 

30587549

 

DOI:

 

10.1158/1078-0432.CCR-18-3230

Introduction to microarray technology-book chapter

Publication in Medical Oncology

Med Oncol. 2018 Oct 5;35(12):152. doi: 10.1007/s12032-018-1212-6.

Association of ERG/PTEN status with biochemical recurrence after radical prostatectomy for clinically localized prostate cancer.

Mehra R1,2,3,4, Salami SS5,6, Lonigro R7, Bhalla R8, Siddiqui J7, Cao X7, Spratt DE5,9, Palapattu GS5,6, Palanisamy N10, Wei JT6, Chinnaiyan AM11,7,5,6,12, Tomlins SA13,14,15.

Author information

Abstract

We have previously demonstrated a significant correlative relationship between PTEN deletion and ERG rearrangement, both in the development of clinically localized prostate cancers and metastases. Herein, we evaluate the cooperative role of ERG and PTEN in oncological outcomes after radical prostatectomy for clinically localized prostate cancer. We evaluated ERG and PTEN status using three previously described cohorts. The first cohort included 235 clinically localized prostate cancer cases represented on tissue microarrays (TMA), evaluated using previously validated FISH assays for ERG and PTEN. The second cohort included 167 cases of clinically localized prostate cancer on TMAs evaluated for PTEN by FISH, and for PTEN and ERG by dual IHC. The third cohort comprised 59 clinically localized prostate cancer cases assessed by array comparative genomic hybridization (aCGH). Kaplan-Meir plots and long rank tests were used to assess the association of ERG and PTEN status with biochemical recurrence after radical prostatectomy for clinically localized prostate cancer. Of the 317 cases eligible for analyses with evaluable ERG and PTEN status, 88 (27.8%) patients developed biochemical recurrence over a median follow-up of 5.7 years. Overall, 45% (142/317) of cases demonstrated ERG rearrangement and 20% (62/317) of cases demonstrated PTEN loss. Hemizygous and homozygous deletion of PTEN was seen in 10% (18/175) and 3% (5/175) of ERG-negative cases, respectively. In contrast, hemizygous and homozygous deletion of PTEN was seen in 11% (15/142) and 17% (24/123) of ERG-positive cases, respectively. PTEN loss (heterozygous or homozygous) was significantly associated with shorter time to biochemical recurrence compared to no PTEN loss (p < 0.001). However, ERG rearrangement versus no rearrangement was not associated with time to PSA recurrence (p = 0.15). Patients who exhibited ERG rearrangement and loss of PTEN had no significant difference in time to recurrence compared to patients with wild-type ERG and loss of PTEN (p = 0.30). Our findings confirm a mutual cooperative role of ERG and PTEN in the pathogenesis of prostate cancer, particularly for homozygous PTEN deletion. ERG did not stratify outcome either alone or in combination with PTEN in this cohort.

KEYWORDS:

ERG; Fluorescent in situ hybridization (FISH); Immunohistochemistry; PTEN; Prostate cancer

PMID:

 

30291535

 

DOI:

 

10.1007/s12032-018-1212-6

Publication in Histopathology

Histopathology. 2018 Sep 21. doi: 10.1111/his.13758. [Epub ahead of print]

Neurofilament is Superior to Cytokeratin 20 in Supporting Cutaneous Origin for Neuroendocrine Carcinoma.

Stanoszek LM1, Chan MP1,2, Palanisamy N3, Carskadon S3, Siddiqui J1, Patel RM1,2, Harms KL2, Lowe L1,2, Fullen DR1,2, Harms PW1,2.

Author information

Abstract

AIM:

Primary cutaneous neuroendocrine carcinoma, or Merkel cell carcinoma (MCC), cannot be distinguished morphologically from small cell neuroendocrine carcinomas (SmCC) from other sites. Immunohistochemistry is required to confirm cutaneous origin, and is also used for detection of sentinel lymph node (SLN) metastases of MCC. Cytokeratin 20 (CK20) expression is commonly used for these purposes, but is negative in some MCC cases, and has unclear specificity. We evaluated immunohistochemistry for neurofilament and CK20 in MCC compared with SmCC from other sites.

METHODS AND RESULTS:

We evaluated neurofilament expression in 55 MCC specimens from 39 unique patients, including 9 CK20-negative MCC tumors. Neurofilament expression was observed in 42/55 (76.4%) MCC cases, including 7/9 (77.8%) CK20-negative MCC cases. Neurofilament was expressed in 9/12 (75%) Merkel cell polyomavirus-positive tumors and 5/10 (50%) virus-negative tumors. Compared to a standard immunohistochemical panel (cytokeratin cocktail and CK20), neurofilament was 87.5% sensitive for detecting SLN metastases. Neurofilament and CK20 expression was also assessed in 61 extracutaneous SmCC from 60 unique patients, with primary sites including lung (27), bladder (18), cervix (3), gastrointestinal tract (3), sinonasal tract (2), and other sites (7). The specificity of neurofilament and CK20 for MCC versus non-cutaneous SmCC was 96.7% and 59.0%, respectively.

CONCLUSIONS:

Neurofilament has superior specificity to CK20 in distinguishing MCC from non-cutaneous SmCC. Neurofilament is frequently expressed in CK20-negative and virus-negative MCC tumors. Limitations of neurofilament immunohistochemistry include lower sensitivity than CK20 and subtle staining in some tumors. However, our findings indicate neurofilament is useful for excluding non-cutaneous SmCC. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.

KEYWORDS:

Merkel cell carcinoma; Merkel cell polyomavirus; cytokeratin 20; neuroendocrine carcinoma; neurofilament; sentinel lymph node; small cell carcinoma

PMID:

 

30239030

 

DOI:

 

10.1111/his.13758

Publication in J Cancer Res Clin Oncol

J Cancer Res Clin Oncol. 2018 Aug 12. doi: 10.1007/s00432-018-2730-5. [Epub ahead of print]

Clinical utility of assessing PTEN and ERG protein expression in prostate cancer patients: a proposed method for risk stratification.

Bismar TA1,2,3,4,5, Hegazy S6, Feng Z7, Yu D8, Donnelly B9,10, Palanisamy N11, Trock BJ7.

Author information

1

Department of Pathology and Laboratory Medicine, University of Calgary-Cumming School of Medicine, Calgary, AB, Canada. tabismar@ucalgary.ca.

2

Departments of Oncology, Biochemistry and Molecular Biology, University of Calgary-Cumming School of Medicine, Calgary, AB, Canada. tabismar@ucalgary.ca.

3

Arnie Charbonneau Cancer Institute, Tom Baker Cancer Center, Calgary, AB, Canada. tabismar@ucalgary.ca.

4

Prostate Cancer Center, Calgary, AB, Canada. tabismar@ucalgary.ca.

5

Rokyview General Hospital, Calgary Laboratory Services, 7007, 14th Street SW, Calgary, AB, T2V 1P9, Canada. tabismar@ucalgary.ca.

6

Department of Pathology and Laboratory Medicine, University of Calgary-Cumming School of Medicine, Calgary, AB, Canada.

7

Brady Urological Institute, John Hopkins School of Medicine, Baltimore, MD, USA.

8

Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.

9

Department of Urology, University of Calgary, Calgary, AB, Canada.

10

Prostate Cancer Center, Calgary, AB, Canada.

11

Department of Urology, Vattikuti Urology Institute, Henry Ford Health System, Detroit, MI, USA.

Abstract

OBJECTIVES:

To assess the prognostic value of ERG and PTEN protein expression as two of the most common genetic aberration in men with prostate cancer managed non-surgically by androgen deprivation therapy (ADT).

MATERIALS AND METHODS:

463 tumor samples were assessed by double immunohistochemistry stains for ERG and PTEN and data correlated with clinical pathological features including, Gleason score, patients' outcome and ADT.

RESULTS:

ERG expression and PTEN protein loss were present in 28.2% and 38% of total patients respectively. There was a significant interplay between ERG and PTEN expression with 21.8% PTEN negative tumors being ERG positive (p < 0.001). Both ERG and PTEN showed significant association with lethal disease in all patients and those treated with prior ADT representing castrate-resistant disease. However, only PTEN remained significant in multivariable proportional hazards regression analysis, when including Gleason score and patients' age. Depending on patient's subgroup, intact positive PTEN intensity showed better cancer-specific survival with HR ranging from 0.25 to 0.4 compared to tumors with loss of PTEN expression. Assessing combined marker status, patients with decreased PTEN intensity without ERG positivity showed the worst clinical outcome compared to those with no PTEN loss and no ERG expression, where they had best clinical outcome. Patients with ERG expression with or without PTEN loss showed intermediate risk in relation to lethal disease.

CONCLUSION:

This study confirms a significant prognostic role for assessing ERG and PTEN in men with prostate cancer. It supports a role for utilizing combined ERG/PTEN status clinically and prospectively for stratifying PCa patients into different prognostic groups.

KEYWORDS:

Androgen deprivation therapy; Cancer-specific mortality; ERG protein expression; Gleason score; Immunohistochemistry; PTEN expression

PMID:

 

30101374

 

DOI:

 

10.1007/s00432-018-2730-5

கை  ஆண்டது 

கையாண்டதால் 

ஆட்சி போனது 

இந்தியா சிறந்தது !

"இந்தி"யா சிறந்தது ?

Publication in Prostate

Prostate. 2018 Jul 26. doi: 10.1002/pros.23704. [Epub ahead of print]

Wnt receptor Frizzled 8 is a target of ERG in prostate cancer.

Chakravarthi BVSK, Chandrashekar DS, Hodigere Balasubramanya SA, Robinson AD, Carskadon S, Rao U, Gordetsky J, Manne U, Netto GJ, Sudarshan S, Palanisamy N, Varambally S.

Prostate cancer (PCa) is one of the most frequently diagnosed cancers among men. Many molecular changes have been detailed during PCa progression. The gene encoding the transcription factor ERG shows recurrent rearrangement, resulting in the overexpression of ERG in the majority of prostate cancers. Overexpression of ERG plays a critical role in prostate oncogenesis and development of metastatic disease. Among the downstream effectors of ERG, Frizzled family member FZD4 has been shown to be a target of ERG. Frizzled-8 (FZD8) has been shown to be involved in PCa bone metastasis. In the present study, we show that the expression of FZD8 is directly correlated with ERG expression in PCa. Furthermore, we show that ERG directly targets and activates FZD8 by binding to its promoter. This activation is specific to ETS transcription factor ERG and not ETV1. We propose that ERG overexpression in PCa leads to induction of Frizzled family member FZD8, which is known to activate the Wnt pathway. Taken together, these findings uncover a novel mechanism for PCa metastasis, and indicate that FZD8 may represent a potential therapeutic target for PCa.
KEYWORDS:
PMID:
 

30051493

 

DOI:

 

10.1002/pros.23704

ERG; Frizzled 8; Wnt signaling; metastasis; prostate cancer

Publication in Histopathology

Histopathology. 2018 Aug;73(2):321-326. doi: 10.1111/his.13526. Epub 2018 May 30.

Pseudosarcomatous myofibroblastic proliferations of the genitourinary tract are genetically different from nodular fasciitis and lack USP6, ROS1 and ETV6 gene rearrangements.

Jebastin JAS, Smith SC, Perry KD, Gupta NS, Alanee S, Carskadon S, Chitale DA, Palanisamy N, Williamson SR.

Abstract
AIMS:
Pseudosarcomatous myofibroblastic proliferations of the genitourinary tract have a debatable relationship with inflammatory myofibroblastic tumour (generally lacking ALK rearrangement); however, they share several overlapping features with nodular fasciitis of soft tissue. As rearrangement of the USP6 gene has been recently recognised as a recurrent alteration in soft tissue nodular fasciitis, and several other alternative gene fusions have been recently recognised in inflammatory myofibroblastic tumour, the aim of this study was to investigate whether USP6, ROS1 or ETV6 rearrangements were present in these lesions (12 cases).

METHODS AND RESULTS:
Fluorescence in-situ hybridisation analysis was performed by the use of bacterial artificial chromosome-derived break-apart probes against USP6, ROS1, and ETV6. Two cases with adequate genetic material from recent paraffin tissue blocks were also tested by use of a solid tumour gene fusion detection assay via next-generation sequencing, targeting >50 known genes involved in recurrent fusions. None of the genitourinary pseudosarcomatous myofibroblastic proliferations was found to harbour USP6 (0/12), ROS1 (0/8) or ETV6 (0/7) rearrangements, and no gene fusions were detected in two cases studied by sequencing.

CONCLUSIONS:
Despite overlap in histological and immunohistochemical features between pseudosarcomatous myofibroblastic proliferation and nodular fasciitis, these tumours lack the recently recognised USP6 rearrangements that occur in nodular fasciitis, as well as alternative fusions found in ALK-negative inflammatory myofibroblastic tumours. At present, this diagnosis remains based primarily on clinical, histological and immunohistochemical features.

© 2018 John Wiley & Sons Ltd.

KEYWORDS:
USP6 ; inflammatory myofibroblastic tumour; pseudosarcomatous myofibroblastic proliferation; soft tissue tumours; urinary bladder

PMID: 29617048 DOI: 10.1111/his.13526

Publication in Oncology Reports

Oncol Rep. 2018 Jun;39(6):2537-2544. doi: 10.3892/or.2018.6342. Epub 2018 Mar 30.

Enrichment and mutation detection of circulating tumor cells from blood samples.

Kou R, Zhao J, Gogoi P, Carskadon S, Chow W, Hwang C, Palanisamy N, Leung C, Wang Y.

Abstract
The potential of circulating tumor cells (CTCs) in the diagnosis and prognosis of cancer patients has become increasingly attractive. However, molecular analysis of CTCs is hindered by low sensitivity and a high level of background leukocytes in CTC enrichment technologies. We have developed a novel protocol using a microfluidic device, which enriches and retrieves CTCs from blood samples. The principle of CTC capturing is that tumor cells are larger and less deformable than normal blood cells. To evaluate the potential of utilizing Celsee PREP100 in CTC molecular analysis, we prepared prostate cancer cell lines PC3 and LNCaP, retrieved the captured cells and analyzed them using PCR amplicon sequencing. We were able to recover an average of 79% of 110‑1,100 PC3 and 60‑1,500 LNCaP cells, and detect the p.K139fs*3 deletion of the p53 gene in PC3 cells and p.T877A mutation of the androgen receptor gene in LNCaP cells. Next, we spiked these two types of cells into normal donor blood samples, captured the cells and analyzed them using PCR amplicon sequencing. The PC3 and LNCaP cells were captured and retrieved with the ratio of captured CTCs to the background leukocytes reaching 1:1.5 for PC3 and 1:2.9 for LNCaP cells. We further revealed that the p.K139fs*3 deletion and p.T877A mutation can be detected in the captured PC3 and LNCaP cells, respectively. We successfully validated this approach using clinical blood samples from patients with metastatic prostate cancer. Our results demonstrated a novel approach for CTC enrichment and illustrated the potential of CTC molecular characterization for diagnosis, prognosis and treatment selection of patients with metastatic malignancy.

PMID: 29620284 PMCID: PMC5983925 DOI: 10.3892/or.2018.6342

Solution to protect endangered species

Humans should completely isolate themselves from the animal habitats- please leave them alone. Let nature decide which species to thrive. 

"Problems are not signs

they are guidelines"

Patents by Inventor Nallasivam Palanisamy

Patents by Inventor Nallasivam Palanisamy

Nallasivam Palanisamy has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

• RNA chimeras in human leukemia and lymphoma

  Patent number: 9657350

  Abstract: Provided herein are kits, compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to recurrent RNA fusions as diagnostic markers and clinical targets for leukemia.

  Type: Grant

  Filed: May 6, 2014

  Date of Patent: May 23, 2017

  Assignee: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

  Inventors: Kojo Elenitoba-Johnson, Thirunavukkarasu Velusamy, Nallasivam Palanisamy, Anagh Sahasrabuddhe, Megan Lim, Arul Chinnaiyan

• RAF GENE FUSIONS

  Publication number: 20170081731

  Abstract: The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to RAF gene fusions as diagnostic markers and clinical targets for cancer.

  Type: Application

  Filed: December 6, 2016

  Publication date: March 23, 2017

  Inventors: Arul Chinnaiyan, Nallasivam Palanisamy, Shanker Kalyana-Sundaram

• RAF gene fusions

  Patent number: 9567644

  Abstract: The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to RAF gene fusions as diagnostic markers and clinical targets for cancer.

  Type: Grant

  Filed: January 5, 2015

  Date of Patent: February 14, 2017

  Assignee: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

  Inventors: Arul Chinnaiyan, Nallasivam Palanisamy, Shanker Kalyana-Sundaram

• RAF GENE FUSIONS

  Publication number: 20150191795

  Abstract: The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to RAF gene fusions as diagnostic markers and clinical targets for cancer.

  Type: Application

  Filed: January 5, 2015

  Publication date: July 9, 2015

  Inventors: Arul Chinnaiyan, Nallasivam Palanisamy, Shanker Kalyana-Sundaram

• RAF gene fusions

  Patent number: 8945556

  Abstract: The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to RAF gene fusions as diagnostic markers and clinical targets for cancer.

  Type: Grant

  Filed: November 18, 2011

  Date of Patent: February 3, 2015

  Assignee: The Regents of The University of Michigan

  Inventors: Arul Chinnaiyan, Nallasivam Palanisamy, Shanker Kalyana-Sundaram

• RNA CHIMERAS IN HUMAN LEUKEMIA AND LYMPHOMA

  Publication number: 20140364481

  Abstract: Provided herein are kits, compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to recurrent RNA fusions as diagnostic markers and clinical targets for leukemia.

  Type: Application

  Filed: May 6, 2014

  Publication date: December 11, 2014

  Applicant: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

  Inventors: Kojo Elenitoba-Johnson, Thirunavukkarasu Velusamy, Nallasivam Palanisamy, Anagh Sahasrabuddhe, Megan Lim, Arul Chinnaiyan

• RAF GENE FUSIONS

  Publication number: 20120142549

  Abstract: The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to RAF gene fusions as diagnostic markers and clinical targets for cancer.

  Type: Application

  Filed: November 18, 2011

  Publication date: June 7, 2012

  Applicant: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

  Inventors: Arul Chinnaiyan, Nallasivam Palanisamy, Shanker Kalyana-Sundaram

• Methods of analyzing chromosomal translocations using fluorescence in situ hybridization (FISH)

  Patent number: 7964345

  Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

  Type: Grant

  Filed: April 5, 2005

  Date of Patent: June 21, 2011

  Assignee: Cancer Genetics, Inc.

  Inventors: Nallasivam Palanisamy, Raju S. Chaganti

• FUSED GENES

  Publication number: 20100285475

  Abstract: There is provided at least one isolated fused gene comprising at least one first gene and/or fragment thereof fused to at least one second gene and/or fragment thereof, wherein at least the first and/or the second gene, independently, is selected from the group consisting of: RCC2, CENPF, ARFGEF2, SULF2, MTAP, ATXN7, BCAS3, RPS6KB1, TMEM49, EAP30, a gene having the nucleotide sequence SEQ ID NO:1, and a gene having the nucleic acid SEQ ID NO:2, or a fragment thereof. There is also provided a diagnostic method and/or a kit for detecting the susceptibility, prognosis, and/or to tumour in a subject.

  Type: Application

  Filed: October 22, 2007

  Publication date: November 11, 2010

  Applicant: AGENCY FOR SCIENCE, TECHNOLOGY AND RESEARCH

  Inventors: Nallasivam Palanisamy, Kalpana Ramnarayanan, Edison T. Liu

• Methods of analyzing chromosomal translocations using fluorescence in situ hybridization (FISH)

  Patent number: 7585964

  Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

  Type: Grant

  Filed: May 14, 2002

  Date of Patent: September 8, 2009

  Assignee: Cancer Genetics, Inc.

  Inventors: Nallasivam Palanisamy, Raju S. Chaganti

• METHODS OF ANALYZING CHROMOSOMAL TRANSLOCATIONS USING FLUORESCENCE IN SITU HYBRIDIZATION (FISH)

  Publication number: 20070166749

  Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

  Type: Application

  Filed: March 12, 2007

  Publication date: July 19, 2007

  Applicant: Cancer Genetics, Inc.

  Inventors: Nallasivam Palanisamy, Raju Chaganti

• Methods of analyzing chromosomal translocations using fluorescence in situ hybridization (FISH)

  Publication number: 20050214842

  Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

  Type: Application

  Filed: April 5, 2005

  Publication date: September 29, 2005

  Applicant: Cancer Genetics, Inc.

  Inventors: Nallasivam Palanisamy, Raju Chaganti

• Methods of analyzing chromosomal translocations using fluorescence in situ hybridization (FISH)

  Publication number: 20020192692

  Abstract: Probes and methods of using the probes to detect chromosomal rearrangements and/or deletions are provided. The methods utilize probes that are free of repeat sequences to provide greater selectivity and sensitivity; methods for producing such probes are also disclosed. The probe sets utilized in the detection methods are designed to hybridize to chromosomes at regions outside known breakpoints, instead of spanning the breakpoint as with conventional FISH methods, and, in some instances, are further designed to bind to regions located outside the genes involved in the rearrangement. Methods utilizing probe sets with two and four colors are also described, as are automated methods for analyzing rearrangements.

  Type: Application

  Filed: May 14, 2002

  Publication date: December 19, 2002

  Applicant: Cancer Genetics, Inc.

  Inventors: Nallasivam Palanisamy, Raju S. Chaganti