Evaluation of molecular inversion probe versus TruSeq® custom methods for targeted next-generation sequencing

Almomani, Rowida; Marchi, Margherita; Sopacua, Maurice; Lindsey, Patrick; Koning, Bart de; Santoro, Silvia; Magri, Stefania; Smeets, Hubert J.M.; Boneschi, Filippo Martinelli; Malik, Rayaz A.; Ziegler, Dan; Hoeijmakers, Janneke G. J.; Bönhof, Gidon J.; Dib‐Hajj, Sulayman D.; Waxman, Stephen G.; Merkies, Ingemar S.J.; Lauria, Giuseppe; Faber, Catharina G.; Gerrits, Monique M.

doi:10.1371/journal.pone.0238467

Cited by 18 publications

(13 citation statements)

References 39 publications

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“…In a recent comparative study, 176 IRD patients were analysed with both smMIPs and TS. The smMIPs approach demonstrated enhanced target coverage (97.3% versus 93.9%) and was five times more cost effective when greater than 500 samples were analysed [ 104 ].…”

Section: Expanding Ird Diagnosis Via Whole-gene or Wgsmentioning

confidence: 99%

Next-Generation Sequencing Applications for Inherited Retinal Diseases

Dockery

Whelan

Humphries

et al. 2021

IJMS

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Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.

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Section: Expanding Ird Diagnosis Via Whole-gene or Wgsmentioning

confidence: 99%

Next-Generation Sequencing Applications for Inherited Retinal Diseases

Dockery

Whelan

Humphries

et al. 2021

IJMS

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“…The number smMIPs per gene and size of targeted coding region per gene have been given in Table S3. All probes, synthesized by Integrated DNA Technologies (IDT, Iowa, ID, USA), were 77-80-mers long, containing extension and ligation arm, joined by a common linker with two universal PCR primer sites, as described before [53]. The smMIPs with a high arm copy count (>5×) and/or common nucleotide polymorphisms (SNPs) (>1%) in the extension and ligation arms were excluded.…”

Section: Gene Panel and Smmips-ngs Protocolmentioning

confidence: 99%

“…SmMIP-NGS was performed as described before [53]. In brief, 50-100 ng of genomic DNA was used for hybridization.…”

Section: Gene Panel and Smmips-ngs Protocolmentioning

confidence: 99%

Peripheral Ion Channel Gene Screening in Painful- and Painless-Diabetic Neuropathy

Ślęczkowska

Almomani

Marchi

et al. 2022

IJMS

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Neuropathic pain is common in diabetic peripheral neuropathy (DN), probably caused by pathogenic ion channel gene variants. Therefore, we performed molecular inversion probes-next generation sequencing of 5 transient receptor potential cation channels, 8 potassium channels and 2 calcium-activated chloride channel genes in 222 painful- and 304 painless-DN patients. Twelve painful-DN (5.4%) patients showed potentially pathogenic variants (five nonsense/frameshift, seven missense, one out-of-frame deletion) in ANO3 (n = 3), HCN1 (n = 1), KCNK18 (n = 2), TRPA1 (n = 3), TRPM8 (n = 3) and TRPV4 (n = 1) and fourteen painless-DN patients (4.6%—three nonsense/frameshift, nine missense, one out-of-frame deletion) in ANO1 (n = 1), KCNK18 (n = 3), KCNQ3 (n = 1), TRPA1 (n = 2), TRPM8 (n = 1), TRPV1 (n = 3) and TRPV4 (n = 3). Missense variants were present in both conditions, presumably with loss- or gain-of-functions. KCNK18 nonsense/frameshift variants were found in painless/painful-DN, making a causal role in pain less likely. Surprisingly, premature stop-codons with likely nonsense-mediated RNA-decay were more frequent in painful-DN. Although limited in number, painful-DN patients with ion channel gene variants reported higher maximal pain during the night and day. Moreover, painful-DN patients with TRP variants had abnormal thermal thresholds and more severe pain during the night and day. Our results suggest a role of ion channel gene variants in neuropathic pain, but functional validation is required.

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“…Genetic sequencing was conducted as previously described (60). In brief, coding exons and exon-flanking intron sequences (±20 bp) of SCN1B-4B, SCN3A, and SCN7A-11A were sequenced by single-molecule molecular inversion probenext-generation sequencing (smMIP-NGS).…”

Section: Single-molecule Molecular Inversion Probe-next-generation Sequencingmentioning

confidence: 99%

A novel gain-of-function sodium channel β2 subunit mutation in idiopathic small fiber neuropathy

Alsaloum

Labau

Sosniak

et al. 2021

Journal of Neurophysiology

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Small fiber neuropathy (SFN) is a common condition affecting thinly myelinated Aδ and unmyelinated C fibers, often resulting in excruciating pain and dysautonomia. SFN has been associated with several conditions, but a significant number of cases have no discernible cause. Recent genetic studies have identified potentially pathogenic gain-of-function mutations in several the pore-forming voltage-gated sodium channel α subunits (NaVs) in a subset of patients with SFN, but the auxiliary sodium channel β subunits have been less implicated in the development of the disease. β subunits modulate NaV trafficking and gating, and several mutations have been linked to epilepsy and cardiac dysfunction. Recently, we provided the first evidence for the contribution of a mutation in the β2-subunit to pain in human painful diabetic neuropathy. Here, we provide the first evidence for the involvement of a sodium channel β subunit mutation in the pathogenesis of SFN with no other known causes. We show, through current-clamp analysis, that the newly-identified Y69H variant of the β2 subunit induces neuronal hyperexcitability in dorsal root ganglion neurons, lowering the threshold for action potential firing and allowing for increased repetitive action potential spiking. Underlying the hyperexcitability induced by the β2-Y69H variant, we demonstrate an upregulation in tetrodotoxin-sensitive, but not tetrodotoxin-resistant sodium currents. This provides the first evidence for the involvement of β2 subunits in SFN and strengthens the link between sodium channel β subunits and the development of neuropathic pain in humans.

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Evaluation of molecular inversion probe versus TruSeq® custom methods for targeted next-generation sequencing

Cited by 18 publications

References 39 publications

Next-Generation Sequencing Applications for Inherited Retinal Diseases

Next-Generation Sequencing Applications for Inherited Retinal Diseases

Peripheral Ion Channel Gene Screening in Painful- and Painless-Diabetic Neuropathy

A novel gain-of-function sodium channel β2 subunit mutation in idiopathic small fiber neuropathy

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