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Choi EJ, Baek IC, Park S, Kim HJ, Kim TG. Development of cost-effective and fast KIR genotyping by multiplex PCR-SSP. HLA 2024; 103:e15191. [PMID: 37688498 DOI: 10.1111/tan.15191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 09/11/2023]
Abstract
Killer-cell immunoglobulin-like receptors (KIR) control natural killer (NK) cell functions by recognizing HLA molecules and modulating the activity of NK cells. The KIR gene cluster contains polymorphic and highly homologous genes. Diversity of the KIR region is achieved through differences in gene content, allelic polymorphism, and gene copy number, which result in unrelated individuals having different KIR genotypes and individualized immune responses that are relevant to multiple aspects of human health and disease. Therefore, KIR genotyping is increasingly used in epidemiological studies. Here, we developed multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP) to compensate for the shortcomings of the conventional PCR-SSP method, which is most commonly used for KIR analysis. Multiplex PCR-SSP method involves six multiplex reactions that detect 16 KIR genes and distinguish variant types of some KIR genes by adding two reactions. The assay was evaluated in a blind survey using a panel of 40 reference DNA standards from the UCLA KIR Exchange Program. The results are 100% concordant with the genotype determined using Luminex-based reverse sequence-specific oligonucleotide typing systems. Additionally, we investigated the currently known 16 KIR genes and their common variants in 120 unrelated Korean individuals. The results were consistent with the KIR genotype previously reported by Hwang et al. This multiplex PCR-SSP is an efficient method for analyzing KIR genotypes in both small- and large-scale studies with minimal labor, reagents, and DNA. Furthermore, by providing a better definition of KIR polymorphisms it can contribute to developments in immunogenetics.
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Affiliation(s)
- Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Silvia Park
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tai-Gyu Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Test of an Improved DNA and RNA Purification Protocol—Importance of Proteinase K and Co-Purified Small RNAs. SEPARATIONS 2022. [DOI: 10.3390/separations9110324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Optimized and reliable DNA/RNA extraction protocols are a vital tool in clinical practice in the context of molecular testing. Here, we present our successful attempt to enhance the quantity of RNA isolated from clinical specimens, which we originally found challenging (breast and testis). We compared several purification methods with special focus on two AllPrep system-based protocols (QIAGEN). Our data suggest that addition of proteinase K may markedly increase RNA and, in some cases, also DNA yield. The extraction kit used, AllPrep DNA/RNA/miRNA universal kit, provides RNA amounts comparable with the phenol-chloroform extraction method; however, part of the final yield consisted of small RNAs, visible as a thick band in the bioanalyzer gel-like image (5S peak). The 5S peak, albeit in some cases dominating the bioanalyzer image, plays only a small role in RT-qPCR analysis, and Qubit or NanoDrop measurements can still be used as a reliable estimate of starting amounts of mRNA for downstream analyses. In conclusion, we showed that implementing a protocol containing a step of proteinase K digestion markedly increases RNA yield. The AllPrep DNA/RNA/miRNA Universal Kit can be successfully used for simultaneous extraction of DNA and total RNA, irrespective of the tissue of origin, and does not present inconveniences related to phenol-chloroform extraction.
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Wu L, Wang W, Zhang J, Wu X, Chen Y, Gu X, Shao H, Li H, Liu W. Detection of Five Types of HPV Genotypes Causing Anogenital Warts (Condyloma Acuminatum) Using PCR-Tm Analysis Technology. Front Microbiol 2022; 13:857410. [PMID: 35655998 PMCID: PMC9152731 DOI: 10.3389/fmicb.2022.857410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Condyloma acuminatum (CA) is a common sexually transmitted disease caused by human papillomavirus (HPV) infection. We established a high-throughput, simple, low-cost, and accurate HPV-typing assay (polymerase chain reaction-melting temperature [PCR-Tm] analysis) to detect HPV in CA. Materials and Methods We detected 280 cervical scraping samples, including positive samples of HPV-6 (26), HPV-11 (12), HPV-16 (22), HPV-42 (18), HPV-43 (25), HPV-multiple (19), HPV- other type (58), and HPV-negative samples (100). All samples were compared by PCR-Tm analysis and a flow fluorescence hybridization assay. Sequencing was used to confirm the results of the PCR-Tm analysis. Results PCR-Tm analysis was specific for each genotype (HPV-6, HPV-11, HPV-16, HPV-42, and HPV-43). The sensitivity of the PCR-Tm analysis assay for each genotype was 103, 103, 103, 103, and 102 copies/reaction, respectively. Most of the 158 samples, including 58 HPV-other type positive and 100 HPV-negative samples tested by the flow fluorescence hybridization assay, were tested negative by PCR-Tm analysis. For the 122 remaining samples, 26 HPV-6, 12 HPV-11, 22 HPV-16, 18 HPV-42, 25 HPV-43, and 19 multiple HPV infections were detected through PCR-Tm analysis. In total, 25 HPV-6, 12 HPV-11, 21 HPV-16, 18 HPV-42, 25 HPV-43, and only 10 multiple HPV infections were detected by the flow fluorescence hybridization assay. The kappa coefficient for the analysis of PCR-Tm analysis and flow fluorescence hybridization assay was 0.940 (P < 0.0001), and the 95% confidence interval of the kappa coefficient was 90.3–97.7%. Conclusion PCR-Tm analysis enabled the detection of HPV-6, HPV-11, HPV-16, HPV-42, and HPV-43, including single and multiple infections.
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Affiliation(s)
- Lixia Wu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Children's Hospital of Soochow University, Medical College of Soochow University, Soochow, China
| | - Weifeng Wang
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Jie Zhang
- Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Xuan Wu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Yan Chen
- Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Xiaoping Gu
- Department of Laboratory Medicine, Shanghai Skin Disease Hospital, Tongji University of Medicine, Shanghai, China
| | - Huaqing Shao
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongsheng Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Weiwei Liu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai Skin Disease Hospital, Tongji University of Medicine, Shanghai, China
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Marin WM, Dandekar R, Augusto DG, Yusufali T, Heyn B, Hofmann J, Lange V, Sauter J, Norman PJ, Hollenbach JA. High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING. PLoS Comput Biol 2021; 17:e1008904. [PMID: 34339413 PMCID: PMC8360517 DOI: 10.1371/journal.pcbi.1008904] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/12/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) complex on chromosome 19 encodes receptors that modulate the activity of natural killer cells, and variation in these genes has been linked to infectious and autoimmune disease, as well as having bearing on pregnancy and transplant outcomes. The medical relevance and high variability of KIR genes makes short-read sequencing an attractive technology for interrogating the region, providing a high-throughput, high-fidelity sequencing method that is cost-effective. However, because this gene complex is characterized by extensive nucleotide polymorphism, structural variation including gene fusions and deletions, and a high level of homology between genes, its interrogation at high resolution has been thwarted by bioinformatic challenges, with most studies limited to examining presence or absence of specific genes. Here, we present the PING (Pushing Immunogenetics to the Next Generation) pipeline, which incorporates empirical data, novel alignment strategies and a custom alignment processing workflow to enable high-throughput KIR sequence analysis from short-read data. PING provides KIR gene copy number classification functionality for all KIR genes through use of a comprehensive alignment reference. The gene copy number determined per individual enables an innovative genotype determination workflow using genotype-matched references. Together, these methods address the challenges imposed by the structural complexity and overall homology of the KIR complex. To determine copy number and genotype determination accuracy, we applied PING to European and African validation cohorts and a synthetic dataset. PING demonstrated exceptional copy number determination performance across all datasets and robust genotype determination performance. Finally, an investigation into discordant genotypes for the synthetic dataset provides insight into misaligned reads, advancing our understanding in interpretation of short-read sequencing data in complex genomic regions. PING promises to support a new era of studies of KIR polymorphism, delivering high-resolution KIR genotypes that are highly accurate, enabling high-quality, high-throughput KIR genotyping for disease and population studies.
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Affiliation(s)
- Wesley M. Marin
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Ravi Dandekar
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Danillo G. Augusto
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Tasneem Yusufali
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | | | | | | | | | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jill A. Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
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