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Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data

a technology of pulmonary fibrosis and biopsies, applied in the field of systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data, can solve the problems of difficult diagnosis of ipf, time-consuming review, and inability to definitively diagnose ip

Inactive Publication Date: 2017-11-23
VERACYTE INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

The present invention provides a method and system for detecting whether a lung tissue sample is positive for usual interstitial pneumonia (UIP) or non-usual interstitial pneumonia (non-UIP) by measuring the expression level of certain transcripts in the sample. This can be useful in diagnosing interstitial lung diseases (ILD) and distinguishing between IPF and NSIP. The method involves comparing the expression level of the transcripts with reference expression levels and using a computer generated classifier to distinguish between UIP and non-UIP. The invention can also be used to detect the presence of other subtypes of ILD and non-diagnostic lung tissue.

Problems solved by technology

IPF can be challenging to diagnose.
Despite histopathologic evaluation, a definitive diagnosis may remain elusive.
Such reviews are time consuming and require patients to be seen at regional centers of recognized expertise.

Method used

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  • Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data
  • Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data
  • Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data

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example 1

Sample Collection, Pathology Diagnosis, and Labeling

[0233]Video-assisted thoracoscopic surgery (VATS) specimens were prospectively collected as a part of an Institutional Review Board (IRB) approved ongoing multi-center clinical protocol, BRonchial sAmple collection for a noVel gEnomic test (BRAVE), sponsored by Veracyte, Inc. (South San Francisco, Calif.). Additional VATS and surgical lung biopsy specimens were obtained from banked sources.

[0234]Following surgery, histology slides were collected, de-identified, and submitted to expert pathology review. Selected slides were scanned to construct a permanent digital file of microscopic images (Aperio, Vista, Calif.). Slides were evaluated according to the central pathology diagnostic process described in FIG. 5, resulting in both sample-level and patient-level pathology diagnoses. Pathology categories are summarized in Table 3. A patient can have more than one sample-level diagnosis (i.e. one per VATS sample per patient, most often on...

example 2

Sample Processing

[0237]Frozen tissue samples were mounted for sectioning using Tissue-Tek O.C.T. medium (Sakura Finetek U.S.A.) and 2×20 μm sections generated using a CM1800 cryostat (Leica Biosystems, Buffalo Grove, Ill.). Tissue curls were immediately immersed in RNAprotect (QIAGEN, Valencia, Calif.), incubated overnight at 4° C. and stored at −80° C. until extraction. Whenever possible, adjacent 5 μm tissue curls were mounted onto glass slides and processed for hematoxylin and eosin (H&E) staining following standard procedures.

[0238]Nucleic acids were extracted using the AllPrep Micro Kit (QIAGEN) according to manufacturer's guidelines. Total RNA yield and quality was determined using Quant-it (Invitrogen) and Pico BioAnalyzer kits (Agilent). Fifteen nanograms of total RNA were amplified using Ovation FFPE WTA System (NuGEN, San Carlos, Calif.), hybridized to GeneChip Gene ST 1.0 (Affymetrix, Santa Clara, Calif.) microarrays, processed and scanned according to the manufacturer's ...

example 3

Next-Generation RNA Sequencing

[0239]Whole transcriptome RNA sequencing was performed on select samples at a targeted minimum read depth of 80 million paired-end reads per sample. Briefly, 10 ng of total RNA was amplified using the Ovation RNASeq System v2 (NuGEN, San Carlos, Calif.) and TruSeq (Illumina, San Diego, Calif.) sequencing libraries were prepared and sequenced on an Illumina HiSeq according to manufacturer's instructions. Raw reads were aligned to the hg19 genome assembly using TopHat2. Gene counts were obtained using HTSeq and normalized in Bioconductor using the varianceStabilizingTransformation function in the DESeq2 package. Raw counts and normalized expression levels were obtained for 55,097 transcripts.

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Abstract

The present invention provides systems, methods, and classifiers for differentiating between samples as usual interstitial pneumonia (UIP) or non-UIP.

Description

CROSS REFERENCE TO RELATED APPLICATIONS[0001]This application claims priority to U.S. Provisional application Ser. No. 62 / 075,328, filed Nov. 5, 2014, and U.S. Provisional application Ser. No. 62 / 130,800, filed Mar. 10, 2015, each of which is incorporated by reference herein in its entirety. This application also incorporates by reference herein in its entirety the entire subject matter of PCT / US2014 / 029029, filed Mar. 14, 2014.DESCRIPTION OF THE TEXT FILE SUBMITTED ELECTRONICALLY[0002]The contents of the text file submitted electronically herewith are incorporated herein by reference in their entirety: A computer readable format copy of the Sequence Listing (filename: VRCT_003_01WO_SeqList_ST25.txt, date recorded: Nov. 5, 2015, file size 64 kilobytes).INTRODUCTION[0003]Interstitial lung diseases (ILD) are a heterogeneous group of acute and chronic bilateral parenchymal pulmonary disorders with similar clinical manifestations, but a wide spectrum of severity and outcome1,2. Among th...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68
CPCC12Q1/6883C12Q2600/158C12Q2600/112C12Q2600/156A61P11/00C12Q1/6806C12Q1/686C12Q1/6874C12Q1/6876
Inventor KENNEDY, GIULIA C.DIGGANS, JAMESHUANG, JINGCHOI, YOONHAKIM, SU YEONPANKRATZ, DANIELPAGAN, MORAIMA
Owner VERACYTE INC
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