Pharmacogenomics analysis was performed by Admera Health (Suzhou, China) using PGxOne® 160 with the Illumina X10 Sequencing System (Illumina Inc., San Diego, CA, USA). STATA computer software (version 12.0, StataCorp LP, College Station, TX, USA) was used to test the Hardy–Weinberg equilibrium, and P<0.05 was considered to be statistically significant.
X10 sequencing system
Manufactured by Illumina
Sourced in United States
The X10 Sequencing System is a high-throughput DNA sequencing instrument developed by Illumina. The core function of the X10 Sequencing System is to automate the process of DNA sequencing, enabling efficient generation of genetic data.
Automatically generated - may contain errors
5 protocols using x10 sequencing system
1
Pharmacogenomics Analysis Using PGxOne® 160
2
Tacrolimus PGx Profiling Protocol
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Tacrolimus concentration was tested using the Emit® 2000 Tacrolimus Assay (Siemens Healthcare Diagnostics Inc., Newark, NJ, USA) with a range of 2.0–30 ng/mL. Pharmacogenomic analysis was performed using TDM residual blood samples, which was measured by Admera Health using a PGxOne®160 via the Illumina X10 Sequencing System. Hardy-Weinberg Equilibrium was determined using STATA version 12.0 (Stata Corp., LP., USA). P<0.05 was considered to indicate a statistically significant difference.
3
Sirolimus Assay and Pharmacogenomic Analysis
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Sirolimus concentrations were tested with the Emit 2000 Sirolimus Assay (Siemens Healthcare Diagnostics Inc.) with range of linear response, 3.5–30 ng/ml, whose values of inter-assay variability [coefficient of variation (CV%)] <4.0%, and values of intra-assay CV (%) <6.2%.
The blood samples used for pharmacogenomic testing came from TDM residual samples, and the analysis was measured by Admera Health (Suzhou, China) with PGxOne®160 via the Illumina X10 Sequencing System. Hardy–Weinberg equilibrium was investigated with STATA computer software (version 12.0, Stata Corp LP, USA) and the value of P <0.05 was considered significant from a statistical point of view.
The blood samples used for pharmacogenomic testing came from TDM residual samples, and the analysis was measured by Admera Health (Suzhou, China) with PGxOne®160 via the Illumina X10 Sequencing System. Hardy–Weinberg equilibrium was investigated with STATA computer software (version 12.0, Stata Corp LP, USA) and the value of P <0.05 was considered significant from a statistical point of view.
4
Targeted Sequencing of Neurodevelopmental Disorder Risk Genes
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In this study, potential NDD risk genes are collected based on the following criteria: (1) genes recorded in the Online Mendelian Inheritance in Man (OMIM) (https://omim.org/ ) are associated with NDDs, mainly including autism, cerebral palsy, mental retardation, and epilepsy; (2) candidate genes in the NPdenovo database [28 (link)]; (3) strong risk genes from the SFARI Gene database (https://gene.sfari.org/ ) [30 (link)]; and (4) genes prioritized in our previous NDD-related studies [25 (link), 26 , 31 (link), 32 (link)]. After removing duplicated genes, 547 target genes were selected (Table S1 ).
A total of 935 unrelated trios (probands and their unaffected parents) and 167 probands without parents were recruited from China. Genomic DNA (1 μg) extracted from whole blood was sheared and assembled into a DNA library prior to targeted sequencing. The Illumina X10 sequencing system (Illumina, San Diego, CA, USA) was used to generate paired-end raw data. This panel resulted in an average depth of 181.46× in target regions, and 98.82% of target bases were covered with depth ≥ 10× on average. This study was approved by the Institutional Review Board of the State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. All subjects who participated in this study provided informed consent prior to sample collection.
A total of 935 unrelated trios (probands and their unaffected parents) and 167 probands without parents were recruited from China. Genomic DNA (1 μg) extracted from whole blood was sheared and assembled into a DNA library prior to targeted sequencing. The Illumina X10 sequencing system (Illumina, San Diego, CA, USA) was used to generate paired-end raw data. This panel resulted in an average depth of 181.46× in target regions, and 98.82% of target bases were covered with depth ≥ 10× on average. This study was approved by the Institutional Review Board of the State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. All subjects who participated in this study provided informed consent prior to sample collection.
5
Identification of NDD Risk Genes
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In this study, potential NDD risk genes are collected based on the following criteria: (1) genes recorded in the Online Mendelian Inheritance in Man (OMIM) (https://omim.org/) are associated with NDDs, mainly including autism, cerebral plasy, mental retardation, and epilepsy, (2) candidate genes in the NPdenovo database[28], (3) strong risk genes from the SFARI Gene database (https://gene.sfari.org/) [30] (link), and (4) genes prioritised in our previous NDD-related studies [25, (link)26, 31, (link)32] (link). After removing duplicated genes, 547 target genes were selected (Table S1).
A total of 935 unrelated trios (probands and their unaffected parents) and 167 probands without parents were recruited from China. Genomic DNA (1 μg) extracted from whole blood was sheared and assembled into a DNA library prior to targeted sequencing. The Illumina X10 sequencing system (Illumina, San Diego, CA, USA) was used to generate paired-end raw data. This panel resulted in an average depth of 181.46X in target regions, and 98.82% of target bases were covered with depth ≥ 10X on average. This study was approved by the Institutional Review Board of the State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. All subjects who participated in this study provided informed consent prior to sample collection.
A total of 935 unrelated trios (probands and their unaffected parents) and 167 probands without parents were recruited from China. Genomic DNA (1 μg) extracted from whole blood was sheared and assembled into a DNA library prior to targeted sequencing. The Illumina X10 sequencing system (Illumina, San Diego, CA, USA) was used to generate paired-end raw data. This panel resulted in an average depth of 181.46X in target regions, and 98.82% of target bases were covered with depth ≥ 10X on average. This study was approved by the Institutional Review Board of the State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. All subjects who participated in this study provided informed consent prior to sample collection.
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