Identification of genetic variants associated with tacrolimus metabolism in kidney transplant recipients by extreme phenotype sampling and next generation sequencing

Abstract Background Disseminated Mycobacterium kansasii infection is rare in kidney transplant recipients. The diagnosis may not be suspected readily due to non-specific clinical presentation. The diagnosis and treatment can be further delayed due to poor sensitivity of culture (especially of extra-pulmonary sites) and slow growth in culture media. Accurate and rapid diagnosis of disseminated M. kansasii infections in transplant recipients is important for antimicrobial management. Methods Two cases of disseminated M. kansasii infections with unusual presentation in which rapid diagnosis was made using the Karius test (KT) are presented. The KT is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test that detects microbial cell-free DNA (mcfDNA). After mcfDNA is extracted and NGS performed, human reads are removed, and remaining sequences are aligned to a curated database of >1400 organisms. Organisms present above a statistical threshold are reported. Results Case 1: A 31-year female kidney transplant recipient presented with a thyroglossal duct cyst, as well as swelling of her right metacarpophalangeal joint and left 3rd finger. AFB culture of the thyroglossal cyst aspiration done on post admission day (PAD) 2 took 27 days to be identified as M. kansasii (on PAD 29) whereas plasma sent for KT on PAD 5 reported a positive test for M. kansasii at 284 molecules/microliter (MPM) in 4 days (on PAD 9). Case 2: A 59-year male kidney transplant recipient presented with generalized weakness, arthralgia, pericardial effusion, cytopenia, weight loss and intermittent fevers. Plasma sent for KT on PAD 12 was reported positive for M. kansasii at 1314 MPM in 3 days (on PAD 15). PET CT done simultaneously was consistent with an infection of an old AV graft in the left upper extremity. The AFB culture of the resected graft was confirmed as M. kansasii in 22 days on PAD 36. After the KT was available (before confirmation of M. kansasii on culture), the first patient underwent modification of empiric treatment and the second patient was started on specific treatment for M. kansasii. Table of M. kansasii cases Rapid diagnosis of disseminated M. kansasii infection Conclusion Open-ended NGS plasma testing for mcfDNA identified disseminated M kansasii infection much earlier than standard microbiology and thus helped in initiation and modification of pathogen directed treatment. Disclosures All Authors: No reported disclosures

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PATHOGENIC GENETIC VARIANTS IDENTIFIED BY TARGETED NEXT-GENERATION SEQUENCING IN SOME UNDEFINED PRIMARY IMMUNODEFICIENCY CASES (IZMIR EXPERIENCE)

10.26226/morressier.594a7d45d462b8028d89348d ◽

2017 ◽

Author(s):

Kutukculer Necil

Keyword(s):

Next Generation Sequencing ◽

Primary Immunodeficiency ◽

Genetic Variants ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Assay of frequency and spectrum of genetic variants in TTN in healthy russian population

Translational Medicine ◽

10.18705/2311-4495-2021-8-5-29-37 ◽

2021 ◽

Vol 8 (5) ◽

pp. 29-37

Author(s):

Yu. A. Vakhrushev ◽

A. A. Kozyreva ◽

S. V. Zhuk ◽

O. P. Rotar ◽

A. A. Kostareva

Keyword(s):

Next Generation Sequencing ◽

Genetic Variants ◽

Sanger Sequencing ◽

Heart Diseases ◽

Genetic Research ◽

Russian Population ◽

Next Generation ◽

Data Bases ◽

International Data ◽

Generation Sequencing

Background. Gene TTN associated with all types of cardiomyopathy, however its large size (294 b.p.) warrants a lot of individual unique genetic variants or variants with low frequency, that aggravates their interpretation. Besides that nowadays there is no data about spectrum of variants in this gene in healthy Russian population. Recognition frequency and spectrum of variants in gene TTN in healthy Russian population will allow us to use it for interpretation results of molecular genetic research for patients with different heart pathology, and define prognosis for different heart diseases.Objective. Recognize frequency and spectrum of single nucleotide and truncating variants in gene TTN in healthy Russian population and compare it with international data bases, and evaluate level of pathogenicity these variants and their distributing across titin structure.Design and methods. 192 men in age 55,8±6,6 years were tested with next-generation sequencing. Identified genetic variants were confirmed by Sanger sequencing. Results. Allele missense variant frequency (with frequency less than 0.1%) in TTN in healthy Russian population amount to 15.1 %, and truncating variants — 0.52 %. 37,9 % of them were variants of unknown significance, 62 % — likely-benign and 0.1 % — benign. There was no pathological and likely-pathological variants. Identified genetic variants distributed throughout the titin structure.Conclusion. Received result is congruent с international data bases and researches. Expended laboratory method (Next generation sequencing and confirmation with Sanger sequencing) can be used both in clinical practice, and in creating data bases of genetic variants in healthy Russian population.

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Clinical results and importance of next-generation sequencing (NGS) in detecting targeted mutations in the treatment of metastatic Lung Cancer: Single center initial results

Medical Science and Discovery ◽

10.36472/msd.v6i12.330 ◽

2019 ◽

Vol 6 (12) ◽

pp. 327-332

Author(s):

Cem Mirili ◽

Çiğdem Kahraman ◽

Ali Yılmaz ◽

Mehmet Bilici ◽

Salim Başol Tekin ◽

...

Keyword(s):

Lung Cancer ◽

Next Generation Sequencing ◽

Genetic Variants ◽

Genetic Variant ◽

Clinical Results ◽

Clinical Effects ◽

Next Generation ◽

Variant Analysis ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Objective: In Lung cancer (LC), which is one of the most deadly cancers, longer survival has been achieved with targeted agents. For this reason, it is important to find the patients who are suitable for targeted therapies. Next-generation sequencing (NGS) is a method that allows multiple genetic variants to be detected simultaneously by performing massive parallel DNA sequencing at the same time. We wanted to reveal the clinical effects and benefits of genetic variant analysis with NGS for our patients. Material and Methods: Patients with stage 4 non-squamous and not otherwise specified (NOS) Non-small cell LC who underwent genetic variant analysis with NGS were included in the study, retrospectively. Results: Total of the 51 patients, 41 (80.4%) were male and the median age was 64 (35-85) years. According to TNM, 21 (41.2%) patients were stage 4A, 30 (58.8%) patients were stage 4B and 39 (76.5%) patients had adenocarcinoma and 12 (23.5%) had NOS histology. NGS analyzes were performed in median 14 days (8-43) and determined 24 pathogenic variants in 17 (%25) patients: 9EGFR (%17,6), 6PIKC3A (%11,7), 5KRAS (%9,8), 2PTEN (%3,9), 1BRAF (%1,9), 1MET (%1,6) (7 of them concomitantly). Cytotoxic chemotherapy was recommended in 41, anti-EGFR agents in 8 (afatinib in 4, erlotinib in 4 patients) patients and anti-BRAF+MEK inhibitor agent (dabrafenib+trametinib) in 1 patient. Conclusion: With the NGS, in just two weeks, both target and resistance genetic variants of our patients were detected at the same time and individualized treatments were applied. In this way, both time and cost were saved.

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1584. Development and Dynamics of Cytomegalovirus UL97 Ganciclovir Resistance Mutations in Transplant Recipients Detected by Next-generation Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.1412 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S495-S496

Author(s):

Isabelle Paula Lodding ◽

Mette Jørgensen ◽

Marc Bennedbæk ◽

Nikolai Kirkby ◽

Klaudia Naegele ◽

...

Keyword(s):

Next Generation Sequencing ◽

Transplant Recipients ◽

Next Generation ◽

Resistance Mutations ◽

Ganciclovir Resistance ◽

Generation Sequencing

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Power and sample size of two-stage extreme phenotype sequencing design for next generation sequencing studies

BMC Bioinformatics ◽

10.1186/1471-2105-14-s17-a16 ◽

2013 ◽

Vol 14 (S17) ◽

Author(s):

Guolian Kang

Keyword(s):

Next Generation Sequencing ◽

Sample Size ◽

Next Generation ◽

Two Stage ◽

Extreme Phenotype ◽

Sequencing Studies ◽

Generation Sequencing

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Performance of next-generation sequencing for detection of clinically actionable genetic variants in cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.11099 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 11099-11099

Author(s):

Mohammed Omar Hussaini ◽

Ian S. Hagemann ◽

Teresa Mary Cox ◽

Christina Lockwood ◽

Karen Seibert ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genetic Variants ◽

Simultaneous Detection ◽

Genetic Alterations ◽

Sequence Variants ◽

Tumor Type ◽

Cancer Genes ◽

Next Generation ◽

Therapeutic Implications ◽

Generation Sequencing

11099 Background: Next-generation sequencing (NGS) allows for simultaneous detection of numerous actionable somatic variants in cancer. We have implemented a clinical NGS panel to detect genetic alterations in 25 genes with established roles in cancer and report here the frequency of clinically actionable genetic variants in a variety of cancer types. Methods: NGS testing was performed in a CAP-certified, CLIA-licensed environment on DNA extracted from FFPE tissue in 209 cases spanning 41 histologic tumor types. DNA was enriched by hybrid capture and sequenced to >1,000x average coverage on Illumina sequencers with 2x101bp or 2x150bp reads. Variants were called using clinically validated parameters using the Genome Analysis Toolkit, Pindel, and the custom-written Clinical Genomicist Workstation. Results: Non-small cell lung cancer (45%), pancreatic cancer (10%), and colorectal cancer (8%) were the most common tumors sent for NGS analysis. An average of 3 (range 1- 16) non-synonymous, non-SNP sequence variants per case (SNVs and indels) were detected in the 130kb exonic target. Variants were most commonly seen in TP53, KRAS, and EGFR. 27% of cases (56/209) had one or more variants with therapeutic implications for the tumor type tested (e.g., EGFR mutation in NSCLC). 15% of cases (32/209) showed actionable variants not generally associated with the malignancy tested (e.g., detection of an activating KITvariant in thymic carcinoma). 10% of cases (21/209) had variants that were prognostically significant but not directly targetable. Some cases (9%) had variants that were prognostic/diagnostic and targetable. In 117 cases (56% of total), no therapeutically or prognostically significant variants were identified. Overall, in 92 cases (44%), NGS testing yielded information with therapeutic (majority), prognostic, or diagnostic ramifications. Conclusions: We found that 44% of unselected cancer cases have clinically relevant sequence variants in a set of 25 commonly mutated cancer genes. Our data suggest that clinical NGS testing may serve as an integral tool in realizing the potential of precision medicine in oncology.

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