1
|
Rojansky R, Marboe CC, Berry GJ. Malignancy following solid organ transplantation: Current techniques for determination of donor versus recipient origin. Transpl Infect Dis 2024:e14330. [PMID: 39003580 DOI: 10.1111/tid.14330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Among the post-transplantation complications that patients may encounter, the transmission of a donor-derived malignant neoplasm is uncommon but potentially life threatening. The determination of donor versus recipient origin is essential particularly in the setting of multiple transplant recipients from the donor. Advances in molecular biology now allow accurate discrimination utilizing routine tissue samples in a timely and cost-effective manner. The techniques are routinely performed in hospital molecular biology laboratories and are also available in commercial labs. The current methodologies are discussed and future possibilities are presented for clinicians caring for solid organ recipients.
Collapse
Affiliation(s)
- Rebecca Rojansky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Charles C Marboe
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|
2
|
Sun L, Liu Q, Li S, Ma G, Wang Z, Ma C, Cong B, Fu L. A new strategy to confirm the identity of tumour tissues using single-nucleotide polymorphisms and next-generation sequencing. Int J Legal Med 2019; 134:399-409. [PMID: 31811377 DOI: 10.1007/s00414-019-02216-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/15/2019] [Indexed: 11/25/2022]
Abstract
With growing cancer morbidity, forensics cases in which archived tumour tissues can be used as biological samples are increasing, and an effective method to identify the body source of tumour tissues is needed. Single nucleotide polymorphisms (SNPs) may be a promising biomarker to identify the source of tumour tissues because of their low mutation rate and small amplicon size. Next-generation sequencing techniques offers the ability to detect hundreds of SNPs in a single run. The Precision ID Identity Panel (Thermo Fisher Scientific, Waltham, MA, USA) detects 90 autosomal SNPs for individual identification and 34 lineage-informative SNPs on Y chromosome using the Ion PGM system (Thermo Fisher Scientific). In this study, we evaluated performance of the panel for individual identification of tumour tissues. One hundred and fifty pairs of tumour tissues and corresponding normal tissues were analysed. Loss of heterozygosity was detected only in tumour tissues. The identity-by-state (IBS) scoring system was adopted to identify the body source of tumour tissues. The IBS score, as well as the number of loci with 2 alleles (A2), 1 allele (A1) and 0 alleles (A0) shared, were analysed within each tumour-normal pair, unrelated individual pairs, parent-offspring pairs and full-sibling pairs. According to the probability distribution, threshold of A2 in the range of 69 to 89 could achieve accuracy > 99% in identifying the source of tumour tissues. Thus, we developed a new strategy (process and criteria) to identify the source of tumour tissues that could be used in practice.
Collapse
Affiliation(s)
- Lijuan Sun
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Qi Liu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Zhandong Wang
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, Xuzhou Cancer Hospital, Xuzhou, China
| | - Chunling Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China.
| | - Lihong Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China.
| |
Collapse
|
3
|
Tseng LH, De Marchi F, Pallavajjalla A, Rodriguez E, Xian R, Belchis D, Gocke CD, Eshleman JR, Illei P, Lin MT. Clinical Validation of Discordant Trunk Driver Mutations in Paired Primary and Metastatic Lung Cancer Specimens. Am J Clin Pathol 2019; 152:570-581. [PMID: 31264684 DOI: 10.1093/ajcp/aqz077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To propose an operating procedure for validation of discordant trunk driver mutations. METHODS Concordance of trunk drivers was examined by next-generation sequencing in 15 patients with two to three metastatic lung cancers and 32 paired primary and metastatic lung cancers. RESULTS Tissue identity was confirmed by genotyping 17 single-nucleotide polymorphisms within the panel. All except three pairs showed concordant trunk drivers. Quality assessment conducted in three primary and metastatic pairs with discordant trunk drivers indicates metastasis from a synchronous or remote lung primary in two patients. Review of literature revealed high discordant rates of EGFR and KRAS mutations, especially when Sanger sequencing was applied to examine primary and lymph node metastatic tumors. CONCLUSIONS Trunk driver mutations are highly concordant in primary and metastatic tumors. Discordance of trunk drivers, once confirmed, may suggest a second primary cancer. Guidelines are recommended to establish standard operating procedures for validation of discordant trunk drivers.
Collapse
Affiliation(s)
- Li-Hui Tseng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Medical Genetics, National Taiwan University Hospital, Taipei
| | - Federico De Marchi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Aparna Pallavajjalla
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Erika Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rena Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Deborah Belchis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Peter Illei
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|
4
|
Pigolkin YI, Dolzhanskiy OV, Korostylev SA, Pal'tseva EM, Fedorov DN. [On the possibility to determine genetic identity of the tissues with malignant tumours imbedded in paraffin blocks]. Sud Med Ekspert 2016; 59:16-19. [PMID: 27239766 DOI: 10.17116/sudmed201659316-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The results of analysis of the literature data were used to develop the forensic medical criteria for the assessment of the suitability of paraffin blocks containing the imbedded malignant tumours for the genetic identification of the tissues. The forensic medical criteria and the algorithm for the preliminary characteristic of the material of interest were proposed to avoid the potential errors. It is not recommended to use gastrointestinal carcinomas, breast tumours, and poorly differentiated ovarian tumours. Also unsuitable is the material formerly exposed to radio- and chemotherapeutic agents or paraffin blocks stored during more than 5-7 years. In the doubtful cases, immunohistochemical studies must be carried out to confirm microsatellite instability. Moreover, the tumour genotype and DNA composition from the patients' blood should be confirmed.
Collapse
Affiliation(s)
- Yu I Pigolkin
- I.M. Sechenov First Moscow State Medical University, Russian Ministry of Health, Moscow, Russia, 119991
| | - O V Dolzhanskiy
- B.V. Petrovsky Russian Research Centre of Surgery,Moscow, Russia, 119991
| | | | - E M Pal'tseva
- B.V. Petrovsky Russian Research Centre of Surgery,Moscow, Russia, 119991
| | - D N Fedorov
- B.V. Petrovsky Russian Research Centre of Surgery,Moscow, Russia, 119991
| |
Collapse
|
5
|
Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD. Identification and Correction of Sample Mix-Ups in Expression Genetic Data: A Case Study. G3 (BETHESDA, MD.) 2015; 5:2177-86. [PMID: 26290572 PMCID: PMC4592999 DOI: 10.1534/g3.115.019778] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/19/2015] [Indexed: 12/04/2022]
Abstract
In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci influencing gene expression) with extremely large effect were used to form a classifier to predict an individual's eQTL genotype based on expression data alone. By considering multiple eQTL and their related transcripts, we identified numerous individuals whose predicted eQTL genotypes (based on their expression data) did not match their observed genotypes, and then went on to identify other individuals whose genotypes did match the predicted eQTL genotypes. The concordance of predictions across six tissues indicated that the problem was due to mix-ups in the genotypes (although we further identified a small number of sample mix-ups in each of the six panels of gene expression microarrays). Consideration of the plate positions of the DNA samples indicated a number of off-by-one and off-by-two errors, likely the result of pipetting errors. Such sample mix-ups can be a problem in any genetic study, but eQTL data allow us to identify, and even correct, such problems. Our methods have been implemented in an R package, R/lineup.
Collapse
Affiliation(s)
- Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Aimee Teo Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706
| | - Brian S Yandell
- Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706 Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Śaunak Sen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94107
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
6
|
Huijsmans CJJ, Poodt J, Damen J, van der Linden JC, Savelkoul PHM, Pruijt JFM, Hilbink M, Hermans MHA. Single nucleotide polymorphism (SNP)-based loss of heterozygosity (LOH) testing by real time PCR in patients suspect of myeloproliferative disease. PLoS One 2012; 7:e38362. [PMID: 22768290 PMCID: PMC3388082 DOI: 10.1371/journal.pone.0038362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 05/03/2012] [Indexed: 02/02/2023] Open
Abstract
During tumor development, loss of heterozygosity (LOH) often occurs. When LOH is preceded by an oncogene activating mutation, the mutant allele may be further potentiated if the wild-type allele is lost or inactivated. In myeloproliferative neoplasms (MPN) somatic acquisition of JAK2V617F may be followed by LOH resulting in loss of the wild type allele. The occurrence of LOH in MPN and other proliferative diseases may lead to a further potentiating the mutant allele and thereby increasing morbidity. A real time PCR based SNP profiling assay was developed and validated for LOH detection of the JAK2 region (JAK2LOH). Blood of a cohort of 12 JAK2V617F-positive patients (n=6 25-50% and n=6>50% JAK2V617F) and a cohort of 81 patients suspected of MPN was stored with EDTA and subsequently used for validation. To generate germ-line profiles, non-neoplastic formalin-fixed paraffin-embedded tissue from each patient was analyzed. Results of the SNP assay were compared to those of an established Short Tandem Repeat (STR) assay. Both assays revealed JAK2LOH in 1/6 patients with 25-50% JAK2V617F. In patients with >50% JAK2V617F, JAK2LOH was detected in 6/6 by the SNP assay and 5/6 patients by the STR assay. Of the 81 patients suspected of MPN, 18 patients carried JAK2V617F. Both the SNP and STR assay demonstrated the occurrence of JAK2LOH in 5 of them. In the 63 JAK2V617F-negative patients, no JAK2LOH was observed by SNP and STR analyses. The presented SNP assay reliably detects JAK2LOH and is a fast and easy to perform alternative for STR analyses. We therefore anticipate the SNP approach as a proof of principle for the development of LOH SNP-assays for other clinically relevant LOH loci.
Collapse
Affiliation(s)
- Cornelis J J Huijsmans
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands.
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Single-nucleotide-polymorphism genotyping of Coxiella burnetii during a Q fever outbreak in The Netherlands. Appl Environ Microbiol 2011; 77:2051-7. [PMID: 21257816 DOI: 10.1128/aem.02293-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coxiella burnetii is the etiological agent of Q fever. Currently, the Netherlands is facing the largest Q fever epidemic ever, with almost 4,000 notified human cases. Although the presence of a hypervirulent strain is hypothesized, epidemiological evidence, such as the animal reservoir(s) and genotype of the C. burnetii strain(s) involved, is still lacking. We developed a single-nucleotide-polymorphism (SNP) genotyping assay directly applicable to clinical samples. Ten discriminatory SNPs were carefully selected and detected by real-time PCR. SNP genotyping appeared to be highly suitable for discrimination of C. burnetii strains and easy to perform with clinical samples. With this new method, we show that the Dutch outbreak is caused by at least 5 different C. burnetii genotypes. SNP typing of 14 human samples from the outbreak revealed the presence of 3 dissimilar genotypes. Two genotypes were also present in livestock at 9 farms in the outbreak area. SNP analyses of bulk milk from 5 other farms, commercial cow milk, and cow colostrum revealed 2 additional genotypes that were not detected in humans. SNP genotyping data from clinical samples clearly demonstrate that at least 5 different C. burnetii genotypes are involved in the Dutch outbreak.
Collapse
|
8
|
Huijsmans CJ, Damen J, van der Linden JC, Savelkoul PH, Hermans MH. Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications. BMC Res Notes 2010; 3:239. [PMID: 20840759 PMCID: PMC2954845 DOI: 10.1186/1756-0500-3-239] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 09/14/2010] [Indexed: 01/02/2023] Open
Abstract
Background A large portion of tissues stored worldwide for diagnostic purposes is formalin-fixed and paraffin-embedded (FFPE). These FFPE-archived tissues are an extremely valuable source for retrospective (genetic) studies. These include mutation screening in cancer-critical genes as well as pathogen detection. In this study we evaluated the impact of several widely used DNA extraction methods on the quality of molecular diagnostics on FFPE tissues. Findings We compared 4 DNA extraction methods from 4 identically processed FFPE mammary-, prostate-, colon- and lung tissues with regard to PCR inhibition, real time SNP detection and amplifiable fragment size. The extraction methods, with and without proteinase K pre-treatment, tested were: 1) heat-treatment, 2) QIAamp DNA-blood-mini-kit, 3) EasyMAG NucliSens and 4) Gentra Capture-Column-kit. Amplifiable DNA fragment size was assessed by multiplexed 200-400-600 bp PCR and appeared highly influenced by the extraction method used. Proteinase K pre-treatment was a prerequisite for proper purification of DNA from FFPE. Extractions with QIAamp, EasyMAG and heat-treatment were found suitable for amplification of fragments up to 400 bp from all tissues, 600 bp amplification was marginally successful (best was QIAamp). QIAamp and EasyMAG extracts were found suitable for downstream real time SNP detection. Gentra extraction was unsuitable. Hands-on time was lowest for heat-treatment, followed by EasyMAG. Conclusions We conclude that the extraction method plays an important role with regard to performance in downstream molecular applications.
Collapse
Affiliation(s)
- Cornelis Jj Huijsmans
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands.
| | | | | | | | | |
Collapse
|
9
|
Abstract
Turnaround time for molecular diagnostic tests is critical in detecting infectious agents, in determining a patient's ability to metabolize a drug or drug class, and in detecting minimal residual disease. These applications would benefit from the development of a point-of-care device for nucleic acid extraction, amplification, and detection. The ideal device would have a low cost per test, use a disposable unit use device for all steps in the assay, be portable, and provide a result that requires no interpretation. The creation of such a device requires miniaturization of current technologies and the use of microfluidics, microarrays, and small-diameter capillary tubes to reduce reagent volumes and simplify heat conduction by convection during nucleic acid amplification. This ideal device may be available in 3 to 5 years and will revolutionize and expand the global availability of molecular diagnostic assays.
Collapse
|