berntpopp published a site update

index.html

@@ -147,6 +147,7 @@ <h2>Objective<a href="index.html#objective" class="anchor-section" aria-label="A
 <h2>Methods<a href="index.html#methods" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <div id="sample-selection-and-preparation" class="section level3 unnumbered hasAnchor">
 <h3>Sample selection and preparation<a href="index.html#sample-selection-and-preparation" class="anchor-section" aria-label="Anchor link to header"></a></h3>
+<p>Archived formalin-fixed paraffin-embedded (FFPE) material was selected from individuals with primary aldosteronism.</p>
 </div>
 <div id="targeted-sanger-sequencing-for-known-mutations" class="section level3 unnumbered hasAnchor">
 <h3>Targeted Sanger sequencing for known mutations<a href="index.html#targeted-sanger-sequencing-for-known-mutations" class="anchor-section" aria-label="Anchor link to header"></a></h3>

search_index.json

@@ -1 +1 @@
-[["index.html", "The apa-sequencing Documentation Preface Objective Methods Results Conclusion Outlook", " The apa-sequencing Documentation Frederike Butz, Bernt Popp, Ute Scholl 2024-05-30 Preface This documentation is intended to describe the apa-sequencing project. Objective Primary aldosteronism (PA) is the most common cause of secondary hypertension and is more common than primary hypertension in causing secondary diseases such as stroke, myocardial infarction, heart and renal failure. It is caused by inappropriately increased, partially autonomous synthesis and secretion of the steroid hormone aldosterone with consequent increased renal and intestinal sodium and water reabsorption and increased potassium secretion. The most common causes are a unilateral benign adrenal tumour (aldosterone-producing adenoma, APA) or bilateral aldosteronism. In recent years, the molecular mechanisms leading to autonomous aldosterone production have become the focus of increasing scientific attention. It has been shown that approximately 95% of all APAs have somatic mutations in known disease genes, mainly affecting ion channels and transporters: About 40% have KCNJ5 (e.g. (Choi et al., 2011)) mutations; CACNA1D is the second most commonly affected gene (about 20%). Other less common somatic mutations include mutations in the ATPases ATP1A1 and ATP2B3 and the gene encoding b-catenin, CTNNB1. Methods Sample selection and preparation Targeted Sanger sequencing for known mutations Analysis of high-throughput sequencing data We implemented a comprehensive workflow for aligning, calling variants, and annotating sequencing data. The raw sequencing data files were obtained from the sequencing provider in FASTQ format. The BWA (Burrows-Wheeler Aligner) tool was used to align the sequences to the hg38 the reference genome. The GATK (Genome Analysis Toolkit) was used for variant calling. We used SnpEff and SnpSift to perform annotations. The GitHub repository contains detailed instructions as well as the complete codebase. Results Conclusion Outlook References Choi, M., Scholl, U. I., Yue, P., Björklund, P., Zhao, B., Nelson-Williams, C., Ji, W., Cho, Y., Patel, A., Men, C. J., Lolis, E., Wisgerhof, M. V., Geller, D. S., Mane, S., Hellman, P., Westin, G., Åkerström, G., Wang, W., Carling, T., & Lifton, R. P. (2011). K \\(^{\\textrm{+}}\\) Channel Mutations in Adrenal Aldosterone-Producing Adenomas and Hereditary Hypertension. Science, 331(6018), 768–772. https://doi.org/10.1126/science.1198785 "],["references.html", "References", " References Choi, M., Scholl, U. I., Yue, P., Björklund, P., Zhao, B., Nelson-Williams, C., Ji, W., Cho, Y., Patel, A., Men, C. J., Lolis, E., Wisgerhof, M. V., Geller, D. S., Mane, S., Hellman, P., Westin, G., Åkerström, G., Wang, W., Carling, T., & Lifton, R. P. (2011). K \\(^{\\textrm{+}}\\) Channel Mutations in Adrenal Aldosterone-Producing Adenomas and Hereditary Hypertension. Science, 331(6018), 768–772. https://doi.org/10.1126/science.1198785 "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
+[["index.html", "The apa-sequencing Documentation Preface Objective Methods Results Conclusion Outlook", " The apa-sequencing Documentation Frederike Butz, Bernt Popp, Ute Scholl 2024-05-30 Preface This documentation is intended to describe the apa-sequencing project. Objective Primary aldosteronism (PA) is the most common cause of secondary hypertension and is more common than primary hypertension in causing secondary diseases such as stroke, myocardial infarction, heart and renal failure. It is caused by inappropriately increased, partially autonomous synthesis and secretion of the steroid hormone aldosterone with consequent increased renal and intestinal sodium and water reabsorption and increased potassium secretion. The most common causes are a unilateral benign adrenal tumour (aldosterone-producing adenoma, APA) or bilateral aldosteronism. In recent years, the molecular mechanisms leading to autonomous aldosterone production have become the focus of increasing scientific attention. It has been shown that approximately 95% of all APAs have somatic mutations in known disease genes, mainly affecting ion channels and transporters: About 40% have KCNJ5 (e.g. (Choi et al., 2011)) mutations; CACNA1D is the second most commonly affected gene (about 20%). Other less common somatic mutations include mutations in the ATPases ATP1A1 and ATP2B3 and the gene encoding b-catenin, CTNNB1. Methods Sample selection and preparation Archived formalin-fixed paraffin-embedded (FFPE) material was selected from individuals with primary aldosteronism. Targeted Sanger sequencing for known mutations Analysis of high-throughput sequencing data We implemented a comprehensive workflow for aligning, calling variants, and annotating sequencing data. The raw sequencing data files were obtained from the sequencing provider in FASTQ format. The BWA (Burrows-Wheeler Aligner) tool was used to align the sequences to the hg38 the reference genome. The GATK (Genome Analysis Toolkit) was used for variant calling. We used SnpEff and SnpSift to perform annotations. The GitHub repository contains detailed instructions as well as the complete codebase. Results Conclusion Outlook References Choi, M., Scholl, U. I., Yue, P., Björklund, P., Zhao, B., Nelson-Williams, C., Ji, W., Cho, Y., Patel, A., Men, C. J., Lolis, E., Wisgerhof, M. V., Geller, D. S., Mane, S., Hellman, P., Westin, G., Åkerström, G., Wang, W., Carling, T., & Lifton, R. P. (2011). K \\(^{\\textrm{+}}\\) Channel Mutations in Adrenal Aldosterone-Producing Adenomas and Hereditary Hypertension. Science, 331(6018), 768–772. https://doi.org/10.1126/science.1198785 "],["references.html", "References", " References Choi, M., Scholl, U. I., Yue, P., Björklund, P., Zhao, B., Nelson-Williams, C., Ji, W., Cho, Y., Patel, A., Men, C. J., Lolis, E., Wisgerhof, M. V., Geller, D. S., Mane, S., Hellman, P., Westin, G., Åkerström, G., Wang, W., Carling, T., & Lifton, R. P. (2011). K \\(^{\\textrm{+}}\\) Channel Mutations in Adrenal Aldosterone-Producing Adenomas and Hereditary Hypertension. Science, 331(6018), 768–772. https://doi.org/10.1126/science.1198785 "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]