Merge pull request #69 from sbslee/0.18.0-dev

0.18.0 dev

Author: sbslee

CHANGELOG.rst

@@ -1,10 +1,23 @@
 Changelog
 *********
 
+0.18.0 (2022-08-12)
+-------------------
+
+* PyPGx now has a citation! Please refer to the publication "`ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation <https://doi.org/10.1371/journal.pone.0272129>`__" by Lee et al., 2022 (Steven is the first author). Fore more details, see the Citation section in README.
+* Update phenotype data and star allele nomenclature for SLCO1B1 in accordance with the latest PharmVar version (v5.2.1). Note that SLCO1B1 was first formally added to PharmVar v5.1 on October 14, 2021. For more details, please refer to the publication "`PharmVar GeneFocus: SLCO1B1 <https://doi.org/10.1002/cpt.2705>`__" by Ramsey et al., 2022 (Steven is a co-author of this paper by the way) and the change log in `the PharmVar SLCO1B1 page <https://www.pharmvar.org/gene/SLCO1B1>`__. The PharmVar-developed SLCO1B1 nomenclature has been incorporated by CPIC 2022 guideline on statin-associated musculoskeletal symptoms.
+* Remove duplicate DYPD entry from ``phenotype-table.csv`` file (i.e. Poor Metabolizer).
+* Fix major bug in :command:`run-chip-pipeline` command where ``--impute`` argument is essentially ignored.
+* :issue:`68`: Fix bug in :meth:`api.utils.estimate_phase_beagle` method when there are no overlapping variants between input VCF and reference panel.
+* :issue:`68`: Update :meth:`api.utils.estimate_phase_beagle` method to warn when statistical phasing is skipped.
+* :issue:`68`: Upgrade Beagle version from v5.2 (beagle.28Jun21.220.jar) to v5.4 (beagle.22Jul22.46e.jar) due to a bug in v5.2.
+* :issue:`68`: Update :meth:`api.utils.estimate_phase_beagle` method to filter out variants with improper allele ('I', 'D', 'N', '.'). Note that this issue is specific to chip data.
+* :issue:`68`: Update :meth:`api.utils.import_variants` method to handle input VCF with duplicate variants. Basically, it will warn the user about it and and only keep the first record. This issue seems to occur frequently with chip data.
+
 0.17.0 (2022-07-12)
 -------------------
 
-* :issue:`63`: Fix bug in :meth:`api.utils.estimate_phase_beagle` when there is only one variant in input VCF and Beagle throws an error.
+* :issue:`63`: Fix bug in :meth:`api.utils.estimate_phase_beagle` method when there is only one variant in input VCF and Beagle throws an error.
 * Update :command:`compare-genotypes` command to print the entire discordant calls when ``--verbose`` is used.
 * Update :command:`compute-copy-number` command to ensure that the samples in CovFrame[ReadDepth] and SampleTable[Statistics] are in the same order.
 * :issue:`64`: Update :meth:`api.utils.import_variants` method to 'diploidize' the input VCF when the target gene is G6PD. This is because some variant callers output haploid genotypes for males for the X chromosome, interfering with downstream analyses.

README.rst

@@ -126,6 +126,34 @@ Your contributions (e.g. feature ideas, pull requests) are most welcome.
 | Email: sbstevenlee@gmail.com
 | License: MIT License
 
+Citation
+========
+
+If you use PyPGx in a published analysis, please report the program version
+and cite the following article:
+
+- Lee et al., 2022. `ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation <https://doi.org/10.1371/journal.pone.0272129>`__. PLOS ONE.
+
+In this article, PyPGx was used to call star alleles for genomic DNA
+reference materials from the Centers for Disease Control and Prevention–based
+`Genetic Testing Reference Materials Coordination Program (GeT-RM)
+<https://pypgx.readthedocs.io/en/latest/glossary.html#
+genetic-testing-reference-materials-coordination-program-get-rm>`__, where it
+showed almost 100% concordance with genotype results from previous works.
+
+The development of PyPGx was heavily inspired by `Stargazer <https://
+stargazer.gs.washington.edu/stargazerweb/>`__, another star-allele calling
+tool developed by Steven when he was in his PhD program at the University of
+Washington. Therefore, please also cite the following articles:
+
+- Lee et al., 2019. `Calling star alleles with Stargazer in 28 pharmacogenes with whole genome sequences <https://doi.org/10.1002/cpt.1552>`__. Clinical Pharmacology & Therapeutics.
+- Lee et al., 2018. `Stargazer: a software tool for calling star alleles from next-generation sequencing data using CYP2D6 as a model <https://doi.org/10.1038/s41436-018-0054-0>`__. Genetics in Medicine.
+
+Below is an incomplete list of publications which have used PyPGx:
+
+- Wroblewski et al., 2022. `Pharmacogenetic variation in Neanderthals and Denisovans and implications for human health and response to medications <https://doi.org/10.1101/2021.11.27.470071>`__. bioRxiv.
+- Botton et al., 2020. `Phased Haplotype Resolution of the SLC6A4 Promoter Using Long-Read Single Molecule Real-Time (SMRT) Sequencing <https://doi.org/10.3390/genes11111333>`__. Genes.
+
 Installation
 ============
 
@@ -183,7 +211,7 @@ dependencies installed.
     SNVs and indels. The program is freely available and published under the
     `GNU General Public License <https://faculty.washington.edu/browning/
     beagle/gpl_license>`__. Users do not need to download Beagle separately
-    because a copy of the software (``beagle.28Jun21.220.jar``) is already
+    because a copy of the software (``beagle.22Jul22.46e.jar``) is already
     included in PyPGx.
 
 .. warning::
@@ -541,7 +569,7 @@ Implemented as ``pypgx run-ngs-pipeline`` in CLI and
 ``pypgx.pipeline.run_ngs_pipeline`` in API, this pipeline is designed for
 processing short-read data (e.g. Illumina). Users must specify whether the
 input data is from whole genome sequencing (WGS) or targeted sequencing
-(custome targeted panel sequencing or whole exome sequencing).
+(custom targeted panel sequencing or whole exome sequencing).
 
 This pipeline supports SV detection based on copy number analysis for genes
 that are known to have SV. Therefore, if the target gene is associated with

docs/create.py

@@ -153,6 +153,34 @@
 | Email: sbstevenlee@gmail.com
 | License: MIT License
 
+Citation
+========
+
+If you use PyPGx in a published analysis, please report the program version
+and cite the following article:
+
+- Lee et al., 2022. `ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation <https://doi.org/10.1371/journal.pone.0272129>`__. PLOS ONE.
+
+In this article, PyPGx was used to call star alleles for genomic DNA
+reference materials from the Centers for Disease Control and Prevention–based
+`Genetic Testing Reference Materials Coordination Program (GeT-RM)
+<https://pypgx.readthedocs.io/en/latest/glossary.html#
+genetic-testing-reference-materials-coordination-program-get-rm>`__, where it
+showed almost 100% concordance with genotype results from previous works.
+
+The development of PyPGx was heavily inspired by `Stargazer <https://
+stargazer.gs.washington.edu/stargazerweb/>`__, another star-allele calling
+tool developed by Steven when he was in his PhD program at the University of
+Washington. Therefore, please also cite the following articles:
+
+- Lee et al., 2019. `Calling star alleles with Stargazer in 28 pharmacogenes with whole genome sequences <https://doi.org/10.1002/cpt.1552>`__. Clinical Pharmacology & Therapeutics.
+- Lee et al., 2018. `Stargazer: a software tool for calling star alleles from next-generation sequencing data using CYP2D6 as a model <https://doi.org/10.1038/s41436-018-0054-0>`__. Genetics in Medicine.
+
+Below is an incomplete list of publications which have used PyPGx:
+
+- Wroblewski et al., 2022. `Pharmacogenetic variation in Neanderthals and Denisovans and implications for human health and response to medications <https://doi.org/10.1101/2021.11.27.470071>`__. bioRxiv.
+- Botton et al., 2020. `Phased Haplotype Resolution of the SLC6A4 Promoter Using Long-Read Single Molecule Real-Time (SMRT) Sequencing <https://doi.org/10.3390/genes11111333>`__. Genes.
+
 Installation
 ============
 
@@ -210,7 +238,7 @@
     SNVs and indels. The program is freely available and published under the
     `GNU General Public License <https://faculty.washington.edu/browning/
     beagle/gpl_license>`__. Users do not need to download Beagle separately
-    because a copy of the software (``beagle.28Jun21.220.jar``) is already
+    because a copy of the software (``beagle.22Jul22.46e.jar``) is already
     included in PyPGx.
 
 .. warning::
@@ -568,7 +596,7 @@
 ``pypgx.pipeline.run_ngs_pipeline`` in API, this pipeline is designed for
 processing short-read data (e.g. Illumina). Users must specify whether the
 input data is from whole genome sequencing (WGS) or targeted sequencing
-(custome targeted panel sequencing or whole exome sequencing).
+(custom targeted panel sequencing or whole exome sequencing).
 
 This pipeline supports SV detection based on copy number analysis for genes
 that are known to have SV. Therefore, if the target gene is associated with

docs/faq.rst

@@ -123,3 +123,23 @@ by excluding GSTT1 from your analysis:
 For more details, please see the following articles:
 :ref:`readme:GRCh37 vs. GRCh38` and :ref:`genes:GRCh38 data for GSTT1`.
 Related GitHub issues: :issue:`65`.
+
+Phase-by-extension algorithm
+============================
+
+This algorithm is used for haplotype phasing rare variants that are not
+present in the reference haplotype panel (i.e. cannot be phased
+statistically). The algorithm does not replace statistical phasing; it’s only
+supplementary. The algorithm utilizes haplotype information obtained by
+statistical phasing and a scoring system to determine which of the two
+haplotypes is more likely to carry the rare variant of interest, based on
+the total number of 'tag' SNPs related to that particular variant and also
+matching the observed haplotype, hence the algorithm’s name 'phasing by
+haplotype extension.' Take CYP2D6*21 as an example, which is defined by
+2580_2581insC (core), 2851C>T (tag), and 4181G>C (tag). Both 2851C>T and
+4181G>C are present in the 1KGP panel and thus statistically phasable, while
+2580_2581insC is not. In order to call a sample with 2580_2581insC as having
+CYP2D6*21, PyPGx will first check which of the two haplotypes contains
+2851C>T and 4181G>C and then assign 2580_2581insC to that haplotype. Note
+that the phase-by-extension algorithm can handle multiallelic sites in
+addition to biallelic sites.

docs/genes.rst

@@ -644,6 +644,7 @@ Resources for ABCG2
 -------------------
 
 - `CPIC® guideline for statins and SLCO1B1, ABCG2, and CYP2C9 <https://cpicpgx.org/guidelines/cpic-guideline-for-statins/>`__
+- `The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin-Associated Musculoskeletal Symptoms <https://ascpt.onlinelibrary.wiley.com/doi/10.1002/cpt.2557>`__
 
 CACNA1S
 =======
@@ -668,6 +669,7 @@ Resources for CACNA1S
 
 - `Annotation of CPIC Guideline for desflurane and CACNA1S, RYR1 <https://www.pharmgkb.org/chemical/PA164749136/guidelineAnnotation/PA166180457>`__
 - `CPIC® Guideline for Potent Volatile Anesthetic Agents and Succinylcholine and RYR1 and CACNA1S <https://cpicpgx.org/guidelines/cpic-guideline-for-ryr1-and-cacna1s/>`__
+- `Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for the Use of Potent Volatile Anesthetic Agents and Succinylcholine in the Context of RYR1 or CACNA1S Genotypes <https://doi.org/10.1002/cpt.1319>`__
 
 CFTR
 ====
@@ -694,6 +696,7 @@ Resources for CFTR
 
 - `Annotation of CPIC Guideline for ivacaftor and CFTR <https://www.pharmgkb.org/chemical/PA165950341/guidelineAnnotation/PA166114461>`__
 - `CPIC® Guideline for Ivacaftor and CFTR <https://cpicpgx.org/guidelines/guideline-for-ivacaftor-and-cftr/>`__
+- `Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for Ivacaftor Therapy in the Context of CFTR Genotype <https://doi.org/10.1038/clpt.2014.54>`__
 
 CYP1A1
 ======
@@ -1222,6 +1225,7 @@ Resources for CYP2C9
 
 - `PharmVar CYP2C9 page <https://www.pharmvar.org/gene/CYP2C9>`__
 - `CPIC® Guideline for NSAIDs based on CYP2C9 genotype <https://cpicpgx.org/guidelines/cpic-guideline-for-nsaids-based-on-cyp2c9-genotype/>`__
+- `The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin-Associated Musculoskeletal Symptoms <https://ascpt.onlinelibrary.wiley.com/doi/10.1002/cpt.2557>`__
 
 CYP2C19
 =======
@@ -2292,6 +2296,7 @@ Resources for IFNL3
 -------------------
 
 - `Annotation of CPIC Guideline for peginterferon alfa-2a,peginterferon alfa-2b,ribavirin and IFNL3 <https://www.pharmgkb.org/guidelineAnnotation/PA166110235>`__
+- `CPIC® Guideline for PEG Interferon-Alpha-Based Regimens and IFNL3 <https://cpicpgx.org/guidelines/guideline-for-peg-interferon-alpha-based-regimens-and-ifnl3/>`__
 
 NUDT15
 ======
@@ -2362,6 +2367,7 @@ Resources for RYR1
 
 - `Annotation of CPIC Guideline for desflurane and CACNA1S, RYR1 <https://www.pharmgkb.org/chemical/PA164749136/guidelineAnnotation/PA166180457>`__
 - `CPIC® Guideline for Potent Volatile Anesthetic Agents and Succinylcholine and RYR1 and CACNA1S <https://cpicpgx.org/guidelines/cpic-guideline-for-ryr1-and-cacna1s/>`__
+- `Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for the Use of Potent Volatile Anesthetic Agents and Succinylcholine in the Context of RYR1 or CACNA1S Genotypes <https://doi.org/10.1002/cpt.1319>`__
 
 SLC22A2
 =======
@@ -2477,26 +2483,25 @@ Diplotype-phenotype mapping is used for phenotype prediction.
 
    * - Phenotype
      - Example
-   * - Possible Increased Function
-     - \*1A/\*35
+   * - Increased Function
+     - \*14/\*14
    * - Normal Function
-     - \*1A/\*1A
+     - \*1/\*1
    * - Possible Decreased Function
-     - \*1A/\*2
+     - \*2/\*15
    * - Decreased Function
-     - \*1A/\*5
-   * - Possible Poor Function
-     - \*2/\*2
+     - \*1/\*5
    * - Poor Function
      - \*5/\*5
    * - Indeterminate
-     - \*1A/\*7
+     - \*2/\*38
 
 Resources for SLCO1B1
 ---------------------
 
 - `PharmVar SLCO1B1 page <https://www.pharmvar.org/gene/SLCO1B1>`__
 - `CPIC® Guideline for Simvastatin and SLCO1B1 <https://cpicpgx.org/guidelines/guideline-for-simvastatin-and-slco1b1/>`__
+- `The Clinical Pharmacogenetics Implementation Consortium Guideline for SLCO1B1, ABCG2, and CYP2C9 genotypes and Statin-Associated Musculoskeletal Symptoms <https://ascpt.onlinelibrary.wiley.com/doi/10.1002/cpt.2557>`__
 
 SULT1A1
 =======