1
|
Green TE, MacGregor D, Carden SM, Harris RV, Hewitt CA, Berkovic SF, Penington AJ, Scheffer IE, Hildebrand MS. Identification of a recurrent mosaic KRAS variant in brain tissue from an individual with nevus sebaceous syndrome. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006133. [PMID: 34649968 PMCID: PMC8751419 DOI: 10.1101/mcs.a006133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/29/2021] [Indexed: 11/24/2022] Open
Abstract
Nevus sebaceous syndrome (NSS) is a rare, multisystem neurocutaneous disorder, characterized by a congenital nevus, and may include brain malformations such as hemimegalencephaly or focal cortical dysplasia, ocular, and skeletal features. It has been associated with several eponyms including Schimmelpenning and Jadassohn. The isolated skin lesion, nevus sebaceous, is associated with postzygotic variants in HRAS or KRAS in all individuals studied. The RAS proteins encode a family of GTPases that form part of the RAS/MAPK signaling pathway, which is critical for cell cycle regulation and differentiation during development. We studied an individual with nevus sebaceous syndrome with an extensive nevus sebaceous, epilepsy, intellectual disability, and hippocampal sclerosis without pathological evidence of a brain malformation. We used high-depth gene panel sequencing and droplet digital polymerase chain reaction (PCR) to detect and quantify RAS/MAPK gene variants in nevus sebaceous and temporal lobe tissue collected during plastic and epilepsy surgery, respectively. A mosaic KRAS c.34G > T; p.(Gly12Cys) variant, also known as G12C, was detected in nevus sebaceous tissue at 25% variant allele fraction (VAF), at the residue most commonly substituted in KRAS. Targeted droplet digital PCR validated the variant and quantified the mosaicism in other tissues. The variant was detected at 33% in temporal lobe tissue but was absent from blood and healthy skin. We provide molecular confirmation of the clinical diagnosis of NSS. Our data extends the histopathological spectrum of KRAS G12C mosaicism beyond nevus sebaceous to involve brain tissue and, more specifically, hippocampal sclerosis.
Collapse
Affiliation(s)
| | - Duncan MacGregor
- Anatomical Pathology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Susan M Carden
- Department of Ophthalmology, The Royal Children's Hospital, Parkville, Victoria, Australia; Department of Ophthalmology, The Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia ; Department of Paediatrics, University of Melbourne,
| | - Rebekah V Harris
- Epilepsy Research Centre, Department of Medicine (Austin Hospital), University of Melbourne, Heidelberg, Victoria, Australia
| | - Chelsee A Hewitt
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine (Austin Hospital), University of Melbourne, Heidelberg, Victoria, Australia
| | - Anthony J Penington
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Murdoch Children's Research Institute ; Plastic and Maxillofacial Surgery Department, The Royal Children's Hospital
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine (Austin Hospital), University of Melbourne, Heidelberg, Victoria, Australia ; Departments of Paediatrics and Neurology, Austin Health, Heidelberg, Victoria, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine (Austin Hospital), University of Melbourne, Heidelberg, Victoria, Australia; Murdoch Children Research Institute, Parkville, Victoria, Australia
| |
Collapse
|
2
|
Prall OWJ, Browning J, Nastevski V, Caporarello S, Bates B, Hewitt CA, Arenas A, Lamb G, Howlett K, Arnolda R, Adeloju R, Stuart S, Xu H, Fellowes A, Fox SB. ROS1 rearrangements in non-small cell lung cancer: screening by immunohistochemistry using proportion of cells staining without intensity and excluding cases with MAPK pathway drivers improves test performance. Pathology 2021; 54:279-285. [PMID: 34635319 DOI: 10.1016/j.pathol.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
Therapeutically actionable ROS1 rearrangements have been described in 1-3% of non-small cell lung cancer (NSCLC). Screening for ROS1 rearrangements is recommended to be by immunohistochemistry (IHC), followed by confirmation with fluorescence in situ hybridisation (FISH) or sequencing. However, in practise ROS1 IHC presents difficulties due to conflicting scoring systems, multiple clones and expression in tumours that are wild-type for ROS1. We assessed ROS1 IHC in 285 consecutive cases of NSCLC with non-squamous histology over a nearly 2-year period. IHC was scored with ROS1 clone D4D6 (n=270), clone SP384 (n=275) or both clones (n=260). Results were correlated with ROS1 break-apart FISH (n=67), ALK status (n=194), and sequence data of EGFR (n=178) and other drivers, where possible. ROS1 expression was detected in 161/285 cases (56.5%), including 13/14 ROS1 FISH-positive cases. There was no ROS1 expression in one ROS1 FISH-positive case in which sequencing detected an ALK-EML4 fusion, but not a ROS1 fusion. The other 13 ROS1 FISH-positive cases showed moderate to strong staining with both IHC clones. However, one case with a TPM3-ROS1 fusion would have been scored as negative with SP384 and D4D6 clones by some previous criteria. ROS1 expression was also detected in 58/285 cases (20.4%) that had driver mutations in genes other than ROS1. A sensitivity of 100% for detecting a ROS1 rearrangement by FISH was achieved by omitting intensity from the IHC scoring criteria and expression in >0% cells with D4D6 or in ≥50% cells with SP384. Excluding cases with driver events in any MAPK pathway gene (e.g., in ALK, EGFR, KRAS, BRAF, ERBB2 and MET) substantially reduced the number of cases proceeding to ROS1 FISH. Only 15.9% of MAPK-negative NSCLC would proceed to FISH for an IHC threshold of >0% cells with D4D6, with a specificity of 42.4%. For a threshold of ≥50% cells with SP384, only 18.5% of MAPK-negative cases would proceed to FISH, with a specificity of 31.4%. Based on our data we suggest an algorithm for screening for ROS1 rearrangements in NSCLC in which ROS1 FISH is only performed in cases that have been demonstrated to lack activating mutations in any MAPK pathway gene by comprehensive sequencing and ALK IHC, and show staining at any intensity in ≥50% of cells with clone SP384, or >0% cells with D4D6.
Collapse
Affiliation(s)
- Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
| | - Judy Browning
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Violeta Nastevski
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Shana Caporarello
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Bindi Bates
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Chelsee A Hewitt
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Andrea Arenas
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Gareth Lamb
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Kerryn Howlett
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Rainier Arnolda
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Roshana Adeloju
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Shani Stuart
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Huiling Xu
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Department of Clinical Pathology, Faculty of Medicine and Dental Science, The University of Melbourne, Parkville, Vic, Australia
| | - Andrew Fellowes
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| |
Collapse
|
3
|
Lee HC, Md Yusof HH, Leong MPY, Zainal Abidin S, Seth EA, Hewitt CA, Vidyadaran S, Nordin N, Scott HS, Cheah PS, Ling KH. Gene and protein expression profiles of JAK-STAT signalling pathway in the developing brain of the Ts1Cje down syndrome mouse model. Int J Neurosci 2019; 129:871-881. [DOI: 10.1080/00207454.2019.1580280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Han-Chung Lee
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Hadri Hadi Md Yusof
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Melody Pui-Yee Leong
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Shahidee Zainal Abidin
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Eryse Amira Seth
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Chelsee A. Hewitt
- Department of Pathology, The Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Sharmili Vidyadaran
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Pathology, Immunology Unit, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Norshariza Nordin
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Hamish S. Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, SA Pathology, Adelaide, Australia
- School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia
- School of Medicine, School of Biological Sciences, University of Adelaide, Adelaide, South Australia
- Centre for Cancer Biology, SA Pathology, Australian Cancer Research Foundation Genomics Facility, Adelaide, Australia
| | - Pike-See Cheah
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - King-Hwa Ling
- Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| |
Collapse
|
4
|
Yusof HH, Lee HC, Seth EA, Wu X, Hewitt CA, Scott HS, Cheah PS, Li YM, Chau DM, Ling KH. Expression Profiling of Notch Signalling Pathway and Gamma-Secretase Activity in the Brain of Ts1Cje Mouse Model of Down Syndrome. J Mol Neurosci 2019; 67:632-642. [PMID: 30758748 DOI: 10.1007/s12031-019-01275-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/05/2019] [Indexed: 01/23/2023]
Abstract
Notch signalling pathway is involved in the proliferation of neural progenitor cells (NPCs), to inhibit neuronal cell commitment and to promote glial cell fate. Notch protein is cleaved by gamma-secretase, a multisubunit transmembrane protein complex that releases the Notch intracellular domain (NICD) and subsequently activates the downstream targets. Down syndrome (DS) individuals exhibit an increased number of glial cells (particularly astrocytes), and reduced number of neurons suggesting the involvement of Notch signalling pathway in the neurogenic-to-gliogenic shift in DS brain. Ts1Cje is a DS mouse model that exhibit similar neuropathology to human DS individuals. To date, the spatiotemporal gene expression of the Notch and gamma-secretase genes have not been characterised in Ts1Cje mouse brain. Understanding the expression pattern of Notch and gamma-secretase genes may provide a better understanding of the underlying mechanism that leads to the shift. Gene expression analysis using RT-qPCR was performed on early embryonic and postnatal development of DS brain. In the developing mouse brain, mRNA expression analysis showed that gamma-secretase members (Psen1, Pen-2, Aph-1b, and Ncstn) were not differentially expressed. Notch2 was found to be downregulated in the developing Ts1Cje brain samples. Postnatal gene expression study showed complex expression patterns and Notch1 and Notch2 genes were found to be significantly downregulated in the hippocampus at postnatal day 30. Results from RT-qPCR analysis from E15.5 neurosphere culture showed an increase of expression of Psen1, and Aph-1b but downregulation of Pen-2 and Ncstn genes. Gamma-secretase activity in Ts1Cje E15.5 neurospheres was significantly increased by fivefold. In summary, the association and the role of Notch and gamma-secretase gene expression throughout development with neurogenic-to-gliogenic shift in Ts1Cje remain undefined and warrant further validation.
Collapse
Affiliation(s)
- Hadri Hadi Yusof
- Genetics & Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Han-Chung Lee
- Genetics & Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Eryse Amira Seth
- Genetics & Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Xiangzhong Wu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chelsee A Hewitt
- Department of Pathology, The Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, SA Pathology, Adelaide, Australia.,School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, Australia.,Australian Cancer Research Foundation Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Pike-See Cheah
- Genetics & Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - De-Ming Chau
- Genetics & Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - King-Hwa Ling
- Genetics & Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia. .,Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
| |
Collapse
|
5
|
Lawrence KE, Lawrence BL, Hickson RE, Hewitt CA, Gedye KR, Fermin LM, Pomroy WE. Associations between Theileria orientalis Ikeda type infection and the growth rates and haematocrit of suckled beef calves in the North Island of New Zealand. N Z Vet J 2018; 67:66-73. [DOI: 10.1080/00480169.2018.1547227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- KE Lawrence
- School of Veterinary Science, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - BL Lawrence
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - RE Hickson
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - CA Hewitt
- School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - KR Gedye
- School of Veterinary Science, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - LM Fermin
- AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton, New Zealand
| | - WE Pomroy
- School of Veterinary Science, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| |
Collapse
|
6
|
Tan KL, Ling KH, Hewitt CA, Cheah PS, Simpson K, Gordon L, Pritchard MA, Smyth GK, Thomas T, Scott HS. Transcriptional profiling of the postnatal brain of the Ts1Cje mouse model of Down syndrome. Genom Data 2015; 2:314-7. [PMID: 26484118 PMCID: PMC4535870 DOI: 10.1016/j.gdata.2014.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 09/22/2014] [Indexed: 11/17/2022]
Abstract
The Ts1Cje mouse model of Down syndrome (DS) has partial trisomy of mouse chromosome 16 (MMU16), which is syntenic to human chromosome 21 (HSA21). It develops various neuropathological features demonstrated by DS patients such as reduced cerebellar volume [1] and altered hippocampus-dependent learning and memory [2,3]. To understand the global gene expression effect of the partially triplicated MMU16 segment on mouse brain development, we performed the spatiotemporal transcriptome analysis of Ts1Cje and disomic control cerebral cortex, cerebellum and hippocampus harvested at four developmental time-points: postnatal day (P)1, P15, P30 and P84. Here, we provide a detailed description of the experimental and analysis procedures of the microarray dataset, which has been deposited in the Gene Expression Omnibus (GSE49050) database.
Collapse
Affiliation(s)
- Kai-Leng Tan
- Neurobiology and Genetics Group, GRMRC-Medical Genetics Laboratory, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia ; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - King-Hwa Ling
- Neurobiology and Genetics Group, GRMRC-Medical Genetics Laboratory, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia ; Walter and Eliza Hall Institute of Medical Research, Victoria, Australia ; Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Chelsee A Hewitt
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia ; Pathology Department, The Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Pike-See Cheah
- Neurobiology and Genetics Group, GRMRC-Medical Genetics Laboratory, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia ; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Ken Simpson
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia
| | - Lavinia Gordon
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia
| | - Melanie A Pritchard
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Gordon K Smyth
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia ; Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Tim Thomas
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia ; Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish S Scott
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia ; Centre for Cancer Biology, University of South Australia, Department of Molecular Pathology, SA Pathology, Adelaide, Australia ; School of Molecular and Biomedical Bioscience, University of Adelaide, Adelaide, Australia ; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, Australia
| |
Collapse
|
7
|
Richter A, Grieu F, Carrello A, Amanuel B, Namdarian K, Rynska A, Lucas A, Michael V, Bell A, Fox SB, Hewitt CA, Do H, McArthur GA, Wong SQ, Dobrovic A, Iacopetta B. A multisite blinded study for the detection of BRAF mutations in formalin-fixed, paraffin-embedded malignant melanoma. Sci Rep 2013; 3:1659. [PMID: 23584600 PMCID: PMC3625889 DOI: 10.1038/srep01659] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 03/25/2013] [Indexed: 12/11/2022] Open
Abstract
Melanoma patients with BRAF mutations respond to treatment with vemurafenib, thus creating a need for accurate testing of BRAF mutation status. We carried out a blinded study to evaluate various BRAF mutation testing methodologies in the clinical setting. Formalin-fixed, paraffin-embedded melanoma samples were macrodissected before screening for mutations using Sanger sequencing, single-strand conformation analysis (SSCA), high resolution melting analysis (HRM) and competitive allele-specific TaqMan® PCR (CAST-PCR). Concordance of 100% was observed between the Sanger sequencing, SSCA and HRM techniques. CAST-PCR gave rapid and accurate results for the common V600E and V600K mutations, however additional assays are required to detect rarer BRAF mutation types found in 3–4% of melanomas. HRM and SSCA followed by Sanger sequencing are effective two-step strategies for the detection of BRAF mutations in the clinical setting. CAST-PCR was useful for samples with low tumour purity and may also be a cost-effective and robust method for routine diagnostics.
Collapse
Affiliation(s)
- Anna Richter
- School of Surgery, University of Western Australia, Nedlands, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Zapparoli GV, Jorissen RN, Hewitt CA, McBean M, Westerman DA, Dobrovic A. Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection. BMC Cancer 2013; 13:206. [PMID: 23617802 PMCID: PMC3658971 DOI: 10.1186/1471-2407-13-206] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/26/2013] [Indexed: 02/03/2023] Open
Abstract
Background The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. Methods We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. Results We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10-4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay. Conclusions QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer.
Collapse
Affiliation(s)
- Giada V Zapparoli
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria 3002, Australia
| | | | | | | | | | | |
Collapse
|
9
|
Leong DW, Komen JC, Hewitt CA, Arnaud E, McKenzie M, Phipson B, Bahlo M, Laskowski A, Kinkel SA, Davey GM, Heath WR, Voss AK, Zahedi RP, Pitt JJ, Chrast R, Sickmann A, Ryan MT, Smyth GK, Thorburn DR, Scott HS. Proteomic and metabolomic analyses of mitochondrial complex I-deficient mouse model generated by spontaneous B2 short interspersed nuclear element (SINE) insertion into NADH dehydrogenase (ubiquinone) Fe-S protein 4 (Ndufs4) gene. J Biol Chem 2012; 287:20652-63. [PMID: 22535952 PMCID: PMC3370248 DOI: 10.1074/jbc.m111.327601] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 04/05/2012] [Indexed: 01/11/2023] Open
Abstract
Eukaryotic cells generate energy in the form of ATP, through a network of mitochondrial complexes and electron carriers known as the oxidative phosphorylation system. In mammals, mitochondrial complex I (CI) is the largest component of this system, comprising 45 different subunits encoded by mitochondrial and nuclear DNA. Humans diagnosed with mutations in the gene NDUFS4, encoding a nuclear DNA-encoded subunit of CI (NADH dehydrogenase ubiquinone Fe-S protein 4), typically suffer from Leigh syndrome, a neurodegenerative disease with onset in infancy or early childhood. Mitochondria from NDUFS4 patients usually lack detectable NDUFS4 protein and show a CI stability/assembly defect. Here, we describe a recessive mouse phenotype caused by the insertion of a transposable element into Ndufs4, identified by a novel combined linkage and expression analysis. Designated Ndufs4(fky), the mutation leads to aberrant transcript splicing and absence of NDUFS4 protein in all tissues tested of homozygous mice. Physical and behavioral symptoms displayed by Ndufs4(fky/fky) mice include temporary fur loss, growth retardation, unsteady gait, and abnormal body posture when suspended by the tail. Analysis of CI in Ndufs4(fky/fky) mice using blue native PAGE revealed the presence of a faster migrating crippled complex. This crippled CI was shown to lack subunits of the "N assembly module", which contains the NADH binding site, but contained two assembly factors not present in intact CI. Metabolomic analysis of the blood by tandem mass spectrometry showed increased hydroxyacylcarnitine species, implying that the CI defect leads to an imbalanced NADH/NAD(+) ratio that inhibits mitochondrial fatty acid β-oxidation.
Collapse
Affiliation(s)
| | - Jasper C. Komen
- the Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | | | - Estelle Arnaud
- the Département de Génétique Médicale, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Matthew McKenzie
- the Centre for Reproduction and Development, Monash Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Belinda Phipson
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Melanie Bahlo
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Adrienne Laskowski
- the Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Sarah A. Kinkel
- From the Molecular Medicine Division
- Immunology Division, and
- the Department of Medical Biology and
| | | | | | - Anne K. Voss
- From the Molecular Medicine Division
- the Department of Medical Biology and
| | - René P. Zahedi
- the Leibniz-Institut für Analytische Wissenschaften e.V., 44227 Dortmund, Germany
| | - James J. Pitt
- VCGS Pathology, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Roman Chrast
- the Département de Génétique Médicale, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Albert Sickmann
- the Leibniz-Institut für Analytische Wissenschaften e.V., 44227 Dortmund, Germany
- the Medizinisches Proteom Center, Ruhr-Universität-Bochum, 44780 Bochum, Germany
| | - Michael T. Ryan
- the Department of Biochemistry, La Trobe University, Bundoora, Victoria 3086, Australia, and
| | - Gordon K. Smyth
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- the Department of Medical Biology and
- Department of Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David R. Thorburn
- the Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Hamish S. Scott
- From the Molecular Medicine Division
- the Department of Medical Biology and
- the Department of Molecular Pathology, Centre for Cancer Biology, SA Pathology, Box 14 Rundle Mall Post Office, Adelaide, South Australia 5000, Australia, and
- the Schools of Medicine and Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
| |
Collapse
|
10
|
Blombery PA, Wong SQ, Hewitt CA, Dobrovic A, Maxwell EL, Juneja S, Grigoriadis G, Westerman DA. Detection of BRAF mutations in patients with hairy cell leukemia and related lymphoproliferative disorders. Haematologica 2011; 97:780-3. [PMID: 22133769 DOI: 10.3324/haematol.2011.054874] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Hairy cell leukemia has been shown to be strongly associated with the BRAF V600E mutation. We screened 59 unenriched archived bone marrow aspirate and peripheral blood samples from 51 patients with hairy cell leukemia using high resolution melting analysis and confirmatory Sanger sequencing. The BRAF V600E mutation was detected in 38 samples (from 36 patients). The BRAF V600E mutation was detected in all samples with disease involvement above the limit of sensitivity of the techniques used. Thirty-three of 34 samples from other hematologic malignancies were negative for BRAF mutations. A BRAF K601E mutation was detected in a patient with splenic marginal zone lymphoma. Our data support the recent finding of a disease defining point mutation in hairy cell leukemia. Furthermore, high resolution melting with confirmatory Sanger sequencing are useful methods that can be employed in routine diagnostic laboratories to detect BRAF mutations in patients with hairy cell leukemia and related lymphoproliferative disorders.
Collapse
Affiliation(s)
- Piers A Blombery
- Peter MacCallum Cancer Centre, Division of Cancer Medicine, East Melbourne, Victoria, Australia
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Abstract
Bisulphite pyrosequencing is a quantitative methodology for the investigation of DNA methylation of sequences up to 100-bp in length. Biotin-labelled, single-stranded PCR products generated from bisulphite-treated DNA are used as a template with an internal primer to perform the pyrosequencing reaction. Nucleotides are added in a predetermined order in each pyrosequencing cycle and the amount of incorporated nucleotide results in a proportional emission of light. DNA methylation ratios are calculated from the levels of light emitted from each nucleotide incorporated at individual CpG positions in a strand-dependent manner. The methylation detection limit at individual CpG sites is approximately 5% and the results are displayed as an average methylation level for each CpG position assayed across all amplification products generated during a PCR reaction. As a consequence, bisulphite pyrosequencing allows the identification of heterogeneous DNA methylation patterns but does not provide information at a single allele resolution. This methodology is suited to analyse short DNA sequences such as those typically extracted from formalin-fixed paraffin-embedded specimens. Nevertheless, longer PCR products can be sequenced by serial bisulphite pyrosequencing, which utilises tandem assays along the amplicon. The general information provided is applicable for all formats of current pyrosequencing instruments, however, a specific protocol for the PyroMark Q24 instrument is provided.
Collapse
Affiliation(s)
- Thomas Mikeska
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
| | | | | | | |
Collapse
|
12
|
Ling KH, Hewitt CA, Beissbarth T, Hyde L, Cheah PS, Smyth GK, Tan SS, Hahn CN, Thomas T, Thomas PQ, Scott HS. Spatiotemporal regulation of multiple overlapping sense and novel natural antisense transcripts at the Nrgn and Camk2n1 gene loci during mouse cerebral corticogenesis. ACTA ACUST UNITED AC 2010; 21:683-97. [PMID: 20693275 DOI: 10.1093/cercor/bhq141] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Nrgn and Camk2n1 are highly expressed in the brain and play an important role in synaptic long-term potentiation via regulation of Ca(2+)/calmodulin-dependent protein kinase II. We have shown that the gene loci for these 2 proteins are actively transcribed in the adult cerebral cortex and feature multiple overlapping transcripts in both the sense and antisense orientations with alternative polyadenylation. These transcripts were upregulated in the adult compared with embryonic and P1.5 mouse cerebral cortices, and transcripts with different 3' untranslated region lengths showed differing expression profiles. In situ hybridization (ISH) analysis revealed spatiotemporal regulation of the Nrgn and Camk2n1 sense and natural antisense transcripts (NATs) throughout cerebral corticogenesis. In addition, we also demonstrated that the expression of these transcripts was organ-specific. Both Nrgn and Camk2n1 sense and NATs were also upregulated in differentiating P19 teratocarcinoma cells. RNA fluorescent ISH analysis confirmed the capability of these NATs to form double-stranded RNA aggregates with the sense transcripts in the cytoplasm of cells obtained from the brain. We propose that the differential regulation of multiple sense and novel overlapping NATs at the Nrgn and Camk2n1 loci will increase the diversity of posttranscriptional regulation, resulting in cell- and time-specific regulation of their gene products during cerebral corticogenesis and function.
Collapse
Affiliation(s)
- King-Hwa Ling
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science, Adelaide, SA 5000, Australia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Hewitt CA, Ling KH, Merson TD, Simpson KM, Ritchie ME, King SL, Pritchard MA, Smyth GK, Thomas T, Scott HS, Voss AK. Gene network disruptions and neurogenesis defects in the adult Ts1Cje mouse model of Down syndrome. PLoS One 2010; 5:e11561. [PMID: 20661276 PMCID: PMC2905390 DOI: 10.1371/journal.pone.0011561] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 05/31/2010] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Down syndrome (DS) individuals suffer mental retardation with further cognitive decline and early onset Alzheimer's disease. METHODOLOGY/PRINCIPAL FINDINGS To understand how trisomy 21 causes these neurological abnormalities we investigated changes in gene expression networks combined with a systematic cell lineage analysis of adult neurogenesis using the Ts1Cje mouse model of DS. We demonstrated down regulation of a number of key genes involved in proliferation and cell cycle progression including Mcm7, Brca2, Prim1, Cenpo and Aurka in trisomic neurospheres. We found that trisomy did not affect the number of adult neural stem cells but resulted in reduced numbers of neural progenitors and neuroblasts. Analysis of differentiating adult Ts1Cje neural progenitors showed a severe reduction in numbers of neurons produced with a tendency for less elaborate neurites, whilst the numbers of astrocytes was increased. CONCLUSIONS/SIGNIFICANCE We have shown that trisomy affects a number of elements of adult neurogenesis likely to result in a progressive pathogenesis and consequently providing the potential for the development of therapies to slow progression of, or even ameliorate the neuronal deficits suffered by DS individuals.
Collapse
Affiliation(s)
- Chelsee A. Hewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Pathology, The Peter MacCallum Cancer Centre, Melbourne, Australia
| | - King-Hwa Ling
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Molecular Pathology, The Centre for Cancer Biology, The Institute of Medical and Veterinary Science and The Hanson Institute, SA Pathology, and The Adelaide Cancer Research Institute, School of Medicine, University of Adelaide, Adelaide, Australia
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Tobias D. Merson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Ken M. Simpson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Matthew E. Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Sarah L. King
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Melanie A. Pritchard
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Hamish S. Scott
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Molecular Pathology, The Centre for Cancer Biology, The Institute of Medical and Veterinary Science and The Hanson Institute, SA Pathology, and The Adelaide Cancer Research Institute, School of Medicine, University of Adelaide, Adelaide, Australia
| | - Anne K. Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| |
Collapse
|
14
|
Ling KH, Hewitt CA, Beissbarth T, Hyde L, Banerjee K, Cheah PS, Cannon PZ, Hahn CN, Thomas PQ, Smyth GK, Tan SS, Thomas T, Scott HS. Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling. Genome Biol 2009; 10:R104. [PMID: 19799774 PMCID: PMC2784319 DOI: 10.1186/gb-2009-10-10-r104] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 07/20/2009] [Accepted: 10/02/2009] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Development of the cerebral cortex requires highly specific spatio-temporal regulation of gene expression. It is proposed that transcriptome profiling of the cerebral cortex at various developmental time points or regions will reveal candidate genes and associated molecular pathways involved in cerebral corticogenesis. RESULTS Serial analysis of gene expression (SAGE) libraries were constructed from C57BL/6 mouse cerebral cortices of age embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4 to 6 months. Hierarchical clustering analysis of 561 differentially expressed transcripts showed regionalized, stage-specific and co-regulated expression profiles. SAGE expression profiles of 70 differentially expressed transcripts were validated using quantitative RT-PCR assays. Ingenuity pathway analyses of validated differentially expressed transcripts demonstrated that these transcripts possess distinctive functional properties related to various stages of cerebral corticogenesis and human neurological disorders. Genomic clustering analysis of the differentially expressed transcripts identified two highly transcribed genomic loci, Sox4 and Sox11, during embryonic cerebral corticogenesis. These loci feature unusual overlapping sense and antisense transcripts with alternative polyadenylation sites and differential expression. The Sox4 and Sox11 antisense transcripts were highly expressed in the brain compared to other mouse organs and are differentially expressed in both the proliferating and differentiating neural stem/progenitor cells and P19 (embryonal carcinoma) cells. CONCLUSIONS We report validated gene expression profiles that have implications for understanding the associations between differentially expressed transcripts, novel targets and related disorders pertaining to cerebral corticogenesis. The study reports, for the first time, spatio-temporally regulated Sox4 and Sox11 antisense transcripts in the brain, neural stem/progenitor cells and P19 cells, suggesting they have an important role in cerebral corticogenesis and neuronal/glial cell differentiation.
Collapse
Affiliation(s)
- King-Hwa Ling
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
- The School of Medicine, The University of Adelaide, SA, 5005, Australia
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, Adelaide, SA 5000, Australia
| | - Chelsee A Hewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
- Current address: Pathology Department, The Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria 3002, Australia
| | - Tim Beissbarth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
- Current address: Department of Medical Statistics (Biostatistics), University of Göttingen, Humboldtalle 32, 37073 Göttingen, Germany
| | - Lavinia Hyde
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
- Current address: The Bioinformatics Unit, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
| | - Kakoli Banerjee
- School of Molecular and Biomedical Science, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Pike-See Cheah
- School of Molecular and Biomedical Science, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia
| | - Ping Z Cannon
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
| | - Christopher N Hahn
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, Adelaide, SA 5000, Australia
| | - Paul Q Thomas
- School of Molecular and Biomedical Science, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
| | - Seong-Seng Tan
- Howard Florey Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tim Thomas
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
| | - Hamish S Scott
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria 3052, Australia
- The School of Medicine, The University of Adelaide, SA, 5005, Australia
- Department of Molecular Pathology, The Institute of Medical and Veterinary Science and The Hanson Institute, Adelaide, SA 5000, Australia
| |
Collapse
|
15
|
Abstract
The validation of multiplex solid-phase fluorescent minisequencing of mitochondrial DNA (mtDNA) for use in forensic casework is presented. Validation included testing of the reliability and species specificity of the technique, analysis of mixed body fluid samples, analysis of samples and substrate controls from previous cases and somatic stability of mtDNA. Animal, bacterial and fungal species extracts were examined and the test did not show cross-reactivity with other species. Hair, blood, saliva, faeces and semen or vaginal samples were tested from five male and five female individuals. For all the samples tested, heteroplasmy was observed only at position 302/309.1. Body fluid mixtures (blood:saliva, semen:saliva, faeces:semen, vaginal:semen) and DNA:DNA mixtures were examined. In total, 189 mixtures were analysed of which one resulted in a hybrid profile consisting of peaks from each of the two donors. The semen fraction of the semen:saliva and vaginal:semen mixtures appeared to be concentrated in the supernatant fraction of the extract thus highlighting the need to extract both the pellet and supernatant fractions of a stain. Control samples, crime stains and their substrate controls from previous cases were examined. Of the 12 loci typed by minisequencing, 11 could be verified by comparison to results from the sequencing method currently in use for casework and no discrepancies were observed between the two. MtDNA minisequencing was found to be a reliable and reproducible technique and its rapid and discriminating nature make it particularly suitable as a screening technique.
Collapse
Affiliation(s)
- J M Morley
- Forensic Science Service, Mitochondrial DNA Unit, London, UK
| | | | | | | | | | | |
Collapse
|
16
|
Abstract
Primary hyperparathyroidism in childhood is rare. Long-standing hypercalcaemia is reported to result in severe and irreversible renal damage. However, renal complications of hyperparathyroidism, particularly nephrocalcinosis are uncommon. We report a 12-year-old girl presenting after three years with extensive nephrocalcinosis and with rapid recovery of renal function.
Collapse
Affiliation(s)
- D G Eaton
- Department of Paediatrics, Heatherwood Hospital, Ascot, Berkshire, UK
| | | |
Collapse
|
17
|
Appadurai IR, Hewitt CA, Gillbe CE. Complete upper airway obstruction. Can J Anaesth 1992; 39:747-8. [PMID: 1394771 DOI: 10.1007/bf03008248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
18
|
Hewitt JK, Fulker DW, Hewitt CA. Genetic architecture of olfactory discriminative avoidance conditioning in Drosophila melanogaster. J Comp Psychol 1983; 97:52-8. [PMID: 6409500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recent claims to have demonstrated associative learning ability in Drosophila melanogaster raise questions about the adaptive significance of behavioral modifiability of this species. In a strain survey and a 9 X 9 half diallel cross study of olfactory discriminative avoidance conditioning, a low narrow heritability and strong directional dominance or heterosis controlling nonrandom phenotypic variation were found. Furthermore, the predicted inbreeding depression and asymmetrical response to bidirectional genetic selection were both observed. The genetic architecture revealed in these experiments is consistent with a close association between this conditioning phenotype and evolutionary fitness. Predictions from this interpretation to the nature of new mutations have been confirmed, and a possible role for conditioning in courtship behavior has been identified.
Collapse
|