Protocol detail

Targeted panel sequencing for congenital hypothyroidism

Find Similar Protocols

Genomic DNA was purified from peripheral blood mononuclear cells using the Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA). Genomic DNA (10 ng/per sample) was used for library preparation, using the DNA prep with an enrichment protocol (Illumina, San Diego, CA, USA) and a custom targeted panel of the 17 congenital hypothyroidism-causative genes TG (NM_003235.4), TPO (NM_000547.5), DUOXA2 (NM_207581.3), DUOX2 (NM_014080.4), SLC5A5 (NM_000453.2), SLC16A2 (NM_006517.4), SLC26A4 (NM_000441.1), TSHR (NM_000369.2), GNAS1 (NM_000516.4), THRB (NM_000461.4), THRA (NM_003250.5), PAX8 (NM_003466.3), NKX2.1 (NM_001079668.2), NKX2.5 (NM_004387.3), FOXE1 (NM_004473.3), IYD (NM_001164694.1), and SECISBP2 (NM_024077.4) [41 (link)]. Next-generation sequencing was performed on the NextSeq 550 platform using the Mid Output kit v2.5 (Illumina). Sequencing coverage of 30x reads was considered to be the minimum requirement for a sequence variant to be considered. Sequence data were processed using custom bioinformatic software pipelines to align reads to the HG19 reference genome. All reported variants were explored using public databases, as well as literature searches. All variants were confirmed by Sanger sequencing on a capillary ABI 3500XL sequencer using the BigDye Terminator v3.1 Cycle Sequencing kit (Thermo-Fisher Scientific, Waltham, MA, USA).

Free full text: Click here

Bernal Barquero C.E., Geysels R.C., Jacques V., Carro G.H., Martín M., Peyret V., Abregú M.C., Papendieck P., Masini-Repiso A.M., Savagner F., Chiesa A.E., Citterio C.E, & Nicola J.P. (2022). Targeted Next-Generation Sequencing of Congenital Hypothyroidism-Causative Genes Reveals Unexpected Thyroglobulin Gene Variants in Patients with Iodide Transport Defect. International Journal of Molecular Sciences, 23(16), 9251.

Publication 2022

Wizard Genomic DNA Purification Kit Mid Output kit v2.5 ABI 3500XL sequencer BigDye Terminator v3.1 Cycle Sequencing kit

Capillary Congenital hypothyroidism Duox2 Genes Genome Library Nkx2 1 Pax8 Peripheral blood mononuclear cells Promega Thra Thrb

Top 5 similar protocols

Variable analysis

independent variables

Genomic DNA purification method (Wizard Genomic DNA Purification Kit)
Library preparation method (DNA prep with an enrichment protocol)
Targeted panel of 17 congenital hypothyroidism-causative genes

dependent variables

Sequence variants in the targeted genes

control variables

Genomic DNA quantity (10 ng per sample)
Minimum sequencing coverage (30x reads)
Reference genome (HG19)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!