Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

Vree, Paula J P de; Wit, Elzo de; Yılmaz, Mehmet; Heijning, Monique van de; Klous, Petra; Verstegen, Marjon J.A.M.; Wan, Yi Ching Esther; Teunissen, Hans; Krijger, Peter H.L.; Geeven, Geert; Eijk, Paul P.; Sie, Daoud; Ylstra, Bauke; Hulsman, Lorette O. M.; Dooren, Marieke F. van; Zutven, Laura J. C. M. van; Ouweland, Ans van den; Verbeek, Sjef; Dijk, Ko Willems van; Cornelissen, Marion; Das, Atze T.; Berkhout, Ben; Sikkema‐Raddatz, Birgit; Berg, Eva van den; Vlies, Pieter van der; Weening, Desireé; Dunnen, Johan T. den; Matusiak, Magdalena; Lamkanfi, Mohamed; Ligtenberg, Marjolijn J. L.; Brugge, Petra ter; Jonkers, Jos; Foekens, John A.; Martens, John W.M.; Luijt, Rob B. van der; Amstel, Hans Kristian Ploos van; Min, Max van; Splinter, Erik; Laat, Wouter de

doi:10.1038/nbt.2959

Cited by 259 publications

(268 citation statements)

References 39 publications

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“…In sample preparation, TLA is comparable with the original 4C approach but with critical adaptations such that not only contact frequencies can be measured but the entire sequence of a locus can be reconstructed based on proximity ligation. TLA can be used to resequence genes and detect variants and rearrangements, gene fusions, and transgene or virus integration sites in an allele-specific manner (de Vree et al 2014).…”

Section: Modeling the 3d Genomementioning

confidence: 99%

The second decade of 3C technologies: detailed insights into nuclear organization

2016

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The relevance of three-dimensional (3D) genome organization for transcriptional regulation and thereby for cellular fate at large is now widely accepted. Our understanding of the fascinating architecture underlying this function is based on microscopy studies as well as the chromosome conformation capture (3C) methods, which entered the stage at the beginning of the millennium. The first decade of 3C methods rendered unprecedented insights into genome topology. Here, we provide an update of developments and discoveries made over the more recent years. As we discuss, established and newly developed experimental and computational methods enabled identification of novel, functionally important chromosome structures. Regulatory and architectural chromatin loops throughout the genome are being cataloged and compared between cell types, revealing tissue invariant and developmentally dynamic loops. Architectural proteins shaping the genome were disclosed, and their mode of action is being uncovered. We explain how more detailed insights into the 3D genome increase our understanding of transcriptional regulation in development and misregulation in disease. Finally, to help researchers in choosing the approach best tailored for their specific research question, we explain the differences and commonalities between the various 3C-derived methods.

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Section: Modeling the 3d Genomementioning

confidence: 99%

The second decade of 3C technologies: detailed insights into nuclear organization

2016

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“…10,11 Targeted locus amplification library A targeted locus amplification library was prepared as previously described. 12 In brief, genomic DNA was crosslinked, enzymatically digested and then re-ligated to create circularized DNA fragments. After de-crosslinking, breakpoint regions were amplified using PCR with anchored primers designed to target regions upstream and downstream of the presumed breakpoints.…”

Section: Whole-genome Jumping Librarymentioning

confidence: 99%

Estrogen-related receptor gamma implicated in a phenotype including hearing loss and mild developmental delay

et al. 2016

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Analysis of chromosomal rearrangements has been highly successful in identifying genes involved in many congenital abnormalities including hearing loss. Herein, we report a subject, designated DGAP242, with congenital hearing loss (HL) and a de novo balanced translocation 46,XX,t(1;5)(q32;q15)dn. Using multiple next-generation sequencing techniques, we obtained high resolution of the breakpoints. This revealed disruption of the orphan receptor ESRRG on chromosome 1, which is differentially expressed in inner ear hair cells and has previously been implicated in HL, and disruption of KIAA0825 on chromosome 5. Given the translocation breakpoints and supporting literature, disruption of ESRRG is the most likely cause for DGAP242's phenotype and implicates ESRRG in a monogenic form of congenital HL, although a putative contributory role for KIAA0825 in the subject's disorder cannot be excluded. European Journal of Human Genetics (2016) 24, 1622-1626; doi:10.1038/ejhg.2016.64; published online 6 July 2016 INTRODUCTIONHearing loss (HL) is one of the most common birth defects, affecting over one in a thousand newborns. Over half of these cases can be attributed to a genetic etiology. 1 Chromosomal abnormalities have been implicated in several genetic forms of congenital HL including Down, Smith-Magenis and Branchio-Oto-Renal syndromes. 2 In cases of congenital HL accompanied with balanced chromosomal abnormalities (BCAs), high resolution of chromosomal breakpoints can reveal genes that have been disrupted, implicating them in auditory pathology. 3 By employing this strategy, the Developmental Genome Anatomy Project (DGAP, dgap.harvard.edu) has successfully resolved the genetic etiology of HL in several cases of BCAs. 4-6 Herein, we report the highresolution breakpoints from a de novo translocation discovered in a 6-year-old female with congenital bilateral sensorineural hearing loss (SNHL) accompanied with a developmental disorder of speech and language.

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“…NGS can find an immunoglobulin-based MRD marker in the majority of patients, it can reach higher sensitivity levels and is a valid strategy to describe tumor clonal heterogeneity and evolution (80,81,94,95). In addition, other NGS-based techniques, such as targetedlocus amplification (TLA), can provide a newly identified, translocation-based MRD marker in patients without an IGH-derived molecular marker, and may help to perform MRD analysis on subsequent follow-up samples (96,97).…”

Section: Future Directions Of Mrd Studies: Novel Tools Tissues and mentioning

confidence: 99%

Personalized Medicine in Lymphoma: Tailoring Treatment According to Minimal Residual Disease

Dogliotti

Ferrero

2017

MRAJ

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Mature B-cell disorders have recently become highly curable diseases thanks to the introduction of new treatment strategies; nonetheless, despite evidence of complete remission, many patients affected by lymphoma or myeloma eventually relapse and need salvage therapy. Minimal residual disease (MRD) detection and quantification is a powerful tool to evaluate treatment efficacy, to stratify patients, and to predict long-term outcome. In fact, in the current landscape of novel, highly efficacious but toxic and often costly targeted therapies, early identification of factors predictive of treatment response or refractoriness is the key to avoid overtreatment of patients and thus also to reduce costs for health care system.In this article, we reviewed the prognostic role of MRD in follicular lymphoma, mantle cell lymphoma and multiple myeloma. We analyzed published clinical studies and available methodologies, and we described the major ongoing studies of MRD-driven tailored treatment in these diseases. Finally, we discussed novel applications and techniques for MRD identification in hematologic malignancies and future directions of MRD-oriented research. In particular, we hypothesized some possible, next-generation, precision medicine trials in lymphoproliferative diseases based on the most promising currently available biomarkers.

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Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

Cited by 259 publications

References 39 publications

The second decade of 3C technologies: detailed insights into nuclear organization

The second decade of 3C technologies: detailed insights into nuclear organization

Estrogen-related receptor gamma implicated in a phenotype including hearing loss and mild developmental delay

Personalized Medicine in Lymphoma: Tailoring Treatment According to Minimal Residual Disease

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