NGS Panel for Circadian Rhythms

A custom NGS panel with 84 genes related to circadian rhythms and melanopsin (Table s1) was based on a commercial kit (RT2 Profiler PCR Array, Qiagen) and designed with the Nextera DNA Flex Library Prep (Illumina Inc., San Diego, CA). Libraries were prepared from total blood’s DNA and were sequenced as 151-bp paired-end reads on NextSeq 500 platform (Illumina Inc., San Diego, CA). BCL files were demultiplexed and converted to the FASTQ format with the Illumina standalone bcl2fastq program (v2.20.0.422). Generated reads were aligned with BWA [50 (link)] to the reference genome hg19, realignment and base quality score recalibration were performed with GATK [51 (link)] and duplicate removal with PicardTools (https://broadinstitute.github.io/picard/). Alignment and coverage statistics were collected with SAM tools [52 (link)] and GATK. Variants were called and filtered by quality with GATK UnifiedGenotyper and VariantFiltration, then annotated with RefSeq using SnpEff [53 (link)].

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Bacalini M.G., Palombo F., Garagnani P., Giuliani C., Fiorini C., Caporali L., Stanzani Maserati M., Capellari S., Romagnoli M., De Fanti S., Benussi L., Binetti G., Ghidoni R., Galimberti D., Scarpini E., Arcaro M., Bonanni E., Siciliano G., Maestri M., Guarnieri B., Martucci M., Monti D., Carelli V., Franceschi C., La Morgia C, & Santoro A. (2021). Association of rs3027178 polymorphism in the circadian clock gene PER1 with susceptibility to Alzheimer’s disease and longevity in an Italian population. GeroScience, 44(2), 881-896.

Publication 2021

RT2 Profiler PCR Array Nextera DNA Flex Library Prep NextSeq 500 platform bcl2fastq program

A genes Blood Circadian rhythms Dna library Genome Melanopsin

Corresponding Organization :

Other organizations : Istituto delle Scienze Neurologiche di Bologna, University of Bologna, Centro San Giovanni di Dio Fatebenefratelli, Istituti di Ricovero e Cura a Carattere Scientifico, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Pisa, University of Florence, N. I. Lobachevsky State University of Nizhny Novgorod

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Variable analysis

independent variables

Custom NGS panel with 84 genes related to circadian rhythms and melanopsin

dependent variables

Variants called and filtered by quality with GATK UnifiedGenotyper and VariantFiltration, then annotated with RefSeq using SnpEff

control variables

Reference genome hg19
Alignment and coverage statistics collected with SAM tools and GATK

Annotations

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