Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae030
Dechao Xu, Aiping Mao, Libao Chen, Le Wu, Yiyi Ma, Changlin Mei
Background: Autosomal dominant polycystic kidney disease (ADPKD) is mainly caused by heterogeneous variants in the PKD1 and PKD2 genes. Genetic analysis of PKD1 has been challenging due to homology with 6 PKD1 pseudogenes and high GC content.
Methods: A single-tube multiplex long-range-PCR and long-read sequencing-based assay termed "comprehensive analysis of ADPKD" (CAPKD) was developed and evaluated in 170 unrelated patients by comparing to control methods including next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification.
Results: CAPKD achieved highly specific analysis of PKD1 with a residual noise ratio of 0.05% for the 6 pseudogenes combined. CAPKD identified PKD1 and PKD2 variants (ranging from variants of uncertain significance to pathogenic) in 160 out of the 170 patients, including 151 single-nucleotide variants (SNVs) and insertion-deletion variants (indels), 6 large deletions, and one large duplication. Compared to NGS, CAPKD additionally identified 2 PKD1 variants (c.78_96dup and c.10729_10732dup). Overall, CAPKD increased the rate of variant detection from 92.9% (158/170) to 94.1% (160/170), and the rate of diagnosis with pathogenic or likely pathogenic variants from 82.4% (140/170) to 83.5% (142/170). CAPKD also directly determined the cis-/trans-configurations in 11 samples with 2 or 3 SNVs/indels, and the breakpoints of 6 large deletions and one large duplication, including 2 breakpoints in the intron 21 AG-repeat of PKD1, which could only be correctly characterized by aligning to T2T-CHM13.
Conclusions: CAPKD represents a comprehensive and specific assay toward full characterization of PKD1 and PKD2 variants, and improves the genetic diagnosis for ADPKD.
{"title":"Comprehensive Analysis of PKD1 and PKD2 by Long-Read Sequencing in Autosomal Dominant Polycystic Kidney Disease.","authors":"Dechao Xu, Aiping Mao, Libao Chen, Le Wu, Yiyi Ma, Changlin Mei","doi":"10.1093/clinchem/hvae030","DOIUrl":"10.1093/clinchem/hvae030","url":null,"abstract":"<p><strong>Background: </strong>Autosomal dominant polycystic kidney disease (ADPKD) is mainly caused by heterogeneous variants in the PKD1 and PKD2 genes. Genetic analysis of PKD1 has been challenging due to homology with 6 PKD1 pseudogenes and high GC content.</p><p><strong>Methods: </strong>A single-tube multiplex long-range-PCR and long-read sequencing-based assay termed \"comprehensive analysis of ADPKD\" (CAPKD) was developed and evaluated in 170 unrelated patients by comparing to control methods including next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification.</p><p><strong>Results: </strong>CAPKD achieved highly specific analysis of PKD1 with a residual noise ratio of 0.05% for the 6 pseudogenes combined. CAPKD identified PKD1 and PKD2 variants (ranging from variants of uncertain significance to pathogenic) in 160 out of the 170 patients, including 151 single-nucleotide variants (SNVs) and insertion-deletion variants (indels), 6 large deletions, and one large duplication. Compared to NGS, CAPKD additionally identified 2 PKD1 variants (c.78_96dup and c.10729_10732dup). Overall, CAPKD increased the rate of variant detection from 92.9% (158/170) to 94.1% (160/170), and the rate of diagnosis with pathogenic or likely pathogenic variants from 82.4% (140/170) to 83.5% (142/170). CAPKD also directly determined the cis-/trans-configurations in 11 samples with 2 or 3 SNVs/indels, and the breakpoints of 6 large deletions and one large duplication, including 2 breakpoints in the intron 21 AG-repeat of PKD1, which could only be correctly characterized by aligning to T2T-CHM13.</p><p><strong>Conclusions: </strong>CAPKD represents a comprehensive and specific assay toward full characterization of PKD1 and PKD2 variants, and improves the genetic diagnosis for ADPKD.</p>","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140287145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae009
Shivaprasad H Sathyanarayana, Madhumala K Sadanandappa, Joel A Lefferts
{"title":"Y Chromosome: The Dark Matter of the Human Genome Unveiled.","authors":"Shivaprasad H Sathyanarayana, Madhumala K Sadanandappa, Joel A Lefferts","doi":"10.1093/clinchem/hvae009","DOIUrl":"https://doi.org/10.1093/clinchem/hvae009","url":null,"abstract":"","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae057
Paul K Hamilton
{"title":"Commentary on Understanding Elevated Vitamin D Measurements to Uncover Hypercalcemia Etiology.","authors":"Paul K Hamilton","doi":"10.1093/clinchem/hvae057","DOIUrl":"https://doi.org/10.1093/clinchem/hvae057","url":null,"abstract":"","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae016
Mark R Girton
{"title":"Study Highlights Difficulties in the Diagnosis of Myelodysplastic Neoplasms (MDS).","authors":"Mark R Girton","doi":"10.1093/clinchem/hvae016","DOIUrl":"10.1093/clinchem/hvae016","url":null,"abstract":"","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae034
Annie Moradian, Elisha Goonatilleke, Tai-Tu Lin, Maya Hatten-Beck, Michelle Emrick, Athena A Schepmoes, Thomas L Fillmore, Michael J MacCoss, Salvatore Sechi, Kimia Sobhani, Randie Little, Kuanysh Kabytaev, Jennifer E van Eyk, Wei-Jun Qian, Andrew N Hoofnagle
Background: The enhanced precision and selectivity of liquid chromatography-tandem mass spectrometry (LC-MS/MS) makes it an attractive alternative to certain clinical immunoassays. Easily transferrable work flows could help facilitate harmonization and ensure high-quality patient care. We aimed to evaluate the interlaboratory comparability of antibody-free multiplexed insulin and C-peptide LC-MS/MS measurements.
Methods: The laboratories that comprise the Targeted Mass Spectrometry Assays for Diabetes and Obesity Research (TaMADOR) consortium verified the performance of a validated peptide-based assay (reproducibility, linearity, and lower limit of the measuring interval [LLMI]). An interlaboratory comparison study was then performed using shared calibrators, de-identified leftover laboratory samples, and reference materials.
Results: During verification, the measurements were precise (2.7% to 3.7%CV), linear (4 to 15 ng/mL for C-peptide and 2 to 14 ng/mL for insulin), and sensitive (LLMI of 0.04 to 0.10 ng/mL for C-peptide and 0.03 ng/mL for insulin). Median imprecision across the 3 laboratories was 13.4% (inter-quartile range [IQR] 11.6%) for C-peptide and 22.2% (IQR 20.9%) for insulin using individual measurements, and 10.8% (IQR 8.7%) and 15.3% (IQR 14.9%) for C-peptide and insulin, respectively, when replicate measurements were averaged. Method comparison with the University of Missouri reference method for C-peptide demonstrated a robust linear correlation with a slope of 1.044 and r2 = 0.99.
Conclusions: Our results suggest that combined LC-MS/MS measurements of C-peptide and insulin are robust and adaptable and that standardization with a reference measurement procedure could allow accurate and precise measurements across sites, which could be important to diabetes research and help patient care in the future.
{"title":"Interlaboratory Comparison of Antibody-Free LC-MS/MS Measurements of C-peptide and Insulin.","authors":"Annie Moradian, Elisha Goonatilleke, Tai-Tu Lin, Maya Hatten-Beck, Michelle Emrick, Athena A Schepmoes, Thomas L Fillmore, Michael J MacCoss, Salvatore Sechi, Kimia Sobhani, Randie Little, Kuanysh Kabytaev, Jennifer E van Eyk, Wei-Jun Qian, Andrew N Hoofnagle","doi":"10.1093/clinchem/hvae034","DOIUrl":"10.1093/clinchem/hvae034","url":null,"abstract":"<p><strong>Background: </strong>The enhanced precision and selectivity of liquid chromatography-tandem mass spectrometry (LC-MS/MS) makes it an attractive alternative to certain clinical immunoassays. Easily transferrable work flows could help facilitate harmonization and ensure high-quality patient care. We aimed to evaluate the interlaboratory comparability of antibody-free multiplexed insulin and C-peptide LC-MS/MS measurements.</p><p><strong>Methods: </strong>The laboratories that comprise the Targeted Mass Spectrometry Assays for Diabetes and Obesity Research (TaMADOR) consortium verified the performance of a validated peptide-based assay (reproducibility, linearity, and lower limit of the measuring interval [LLMI]). An interlaboratory comparison study was then performed using shared calibrators, de-identified leftover laboratory samples, and reference materials.</p><p><strong>Results: </strong>During verification, the measurements were precise (2.7% to 3.7%CV), linear (4 to 15 ng/mL for C-peptide and 2 to 14 ng/mL for insulin), and sensitive (LLMI of 0.04 to 0.10 ng/mL for C-peptide and 0.03 ng/mL for insulin). Median imprecision across the 3 laboratories was 13.4% (inter-quartile range [IQR] 11.6%) for C-peptide and 22.2% (IQR 20.9%) for insulin using individual measurements, and 10.8% (IQR 8.7%) and 15.3% (IQR 14.9%) for C-peptide and insulin, respectively, when replicate measurements were averaged. Method comparison with the University of Missouri reference method for C-peptide demonstrated a robust linear correlation with a slope of 1.044 and r2 = 0.99.</p><p><strong>Conclusions: </strong>Our results suggest that combined LC-MS/MS measurements of C-peptide and insulin are robust and adaptable and that standardization with a reference measurement procedure could allow accurate and precise measurements across sites, which could be important to diabetes research and help patient care in the future.</p>","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140317948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae060
Mariam T Mathew, Yassmine M N Akkari
{"title":"Optical Genome Mapping in Prenatal Diagnosis: Democratizing Comprehensive Cytogenomic Testing.","authors":"Mariam T Mathew, Yassmine M N Akkari","doi":"10.1093/clinchem/hvae060","DOIUrl":"10.1093/clinchem/hvae060","url":null,"abstract":"","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140853864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae044
Umair Sajid, Dennis Orton, Martin Kaufmann, Glenville Jones, Gregory A Kline
{"title":"Understanding Elevated Vitamin D Measurements to Uncover Hypercalcemia Etiology.","authors":"Umair Sajid, Dennis Orton, Martin Kaufmann, Glenville Jones, Gregory A Kline","doi":"10.1093/clinchem/hvae044","DOIUrl":"https://doi.org/10.1093/clinchem/hvae044","url":null,"abstract":"","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae069
Melanie L Yarbrough, Rebekah E Dumm, Lynn Bry, Brendan J Kelly, Drew Schwartz, Aayushi Uberoi
{"title":"Microbiome-Based Diagnostics for Disease: Where Are We Now and Where Are We Headed?","authors":"Melanie L Yarbrough, Rebekah E Dumm, Lynn Bry, Brendan J Kelly, Drew Schwartz, Aayushi Uberoi","doi":"10.1093/clinchem/hvae069","DOIUrl":"10.1093/clinchem/hvae069","url":null,"abstract":"","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1093/clinchem/hvae054
Nader Rifai, William Meredith, Kevin Brown, Sarah A Erdahl, Paul J Jannetto
{"title":"High Lead Levels in 2 Independent and Authenticated Locks of Beethoven's Hair.","authors":"Nader Rifai, William Meredith, Kevin Brown, Sarah A Erdahl, Paul J Jannetto","doi":"10.1093/clinchem/hvae054","DOIUrl":"10.1093/clinchem/hvae054","url":null,"abstract":"","PeriodicalId":10690,"journal":{"name":"Clinical chemistry","volume":null,"pages":null},"PeriodicalIF":7.1,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140852994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}