Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

BACKGROUND Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. RESULTS Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2'antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). CONCLUSIONS Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renalcell carcinoma consisted of at least three subtypes based on molecular and phenotypic features

spacetelescope/wiimatch: Maintenance release

Optimal "matching" of weighted N-dimensional image intensity data using (multivariate) polynomial

spacetelescope/stsynphot_refactor: 1.3.0 Release Notes

<p>Also see <code>CHANGES.rst</code>.</p> <h2>What's Changed</h2> <ul> <li>TST: asdf is bumping numpy in oldest deps so we need to pin it by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/177</li> <li>remove usages of deprecated <code>codecov</code> package by @zacharyburnett in https://github.com/spacetelescope/stsynphot_refactor/pull/178</li> <li>remove unsupported <code>system_packages</code> RTD config setting by @zacharyburnett in https://github.com/spacetelescope/stsynphot_refactor/pull/180</li> <li>NumPy 2.0 compatibility by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/181</li> <li>TST: Bump checkout version and add Python 3.12 by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/182</li> <li>TST: Fix devdeps by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/183</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/spacetelescope/stsynphot_refactor/compare/1.2.0...1.3.0</p&gt

spacetelescope/stsynphot_refactor: 1.3.0 Release Notes

<p>Also see <code>CHANGES.rst</code>.</p> <h2>What's Changed</h2> <ul> <li>TST: asdf is bumping numpy in oldest deps so we need to pin it by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/177</li> <li>remove usages of deprecated <code>codecov</code> package by @zacharyburnett in https://github.com/spacetelescope/stsynphot_refactor/pull/178</li> <li>remove unsupported <code>system_packages</code> RTD config setting by @zacharyburnett in https://github.com/spacetelescope/stsynphot_refactor/pull/180</li> <li>NumPy 2.0 compatibility by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/181</li> <li>TST: Bump checkout version and add Python 3.12 by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/182</li> <li>TST: Fix devdeps by @pllim in https://github.com/spacetelescope/stsynphot_refactor/pull/183</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/spacetelescope/stsynphot_refactor/compare/1.2.0...1.3.0</p&gt

spacetelescope/tweakwcs: Maintenance release: Improved compatibility with numpy 2.0. Minor bug fixes and improvements

Algorithms for matching and aligning catalogs and for tweaking the WCS so as to minimize catalog mismatch error

spacetelescope/stginga: 1.4.0 Release Notes

<p>Also see <code>CHANGES.rst</code>.</p> <h2>What's Changed</h2> <ul> <li>MNT: Replace deprecated dtypes in numpy 1.21 by @pllim in https://github.com/spacetelescope/stginga/pull/219</li> <li>MNT: Do not use enable_deprecations_as_exceptions by @pllim in https://github.com/spacetelescope/stginga/pull/221</li> <li>Fix deprecated scipy import by @pllim in https://github.com/spacetelescope/stginga/pull/222</li> <li>TST: Update workflow versions and use built-in cancel by @pllim in https://github.com/spacetelescope/stginga/pull/223</li> <li>Replace ImageViewCanvas with CanvasView by @ejeschke in https://github.com/spacetelescope/stginga/pull/225</li> <li>use canonical filename of RTD configuration and enable <code>nitpicky</code> mode by @zacharyburnett in https://github.com/spacetelescope/stginga/pull/226</li> <li>Force drawn circle to have a minimum radius of 1 px by @ejeschke in https://github.com/spacetelescope/stginga/pull/228</li> <li>BUG: Like PR 228 but for BackgroundSub by @pllim in https://github.com/spacetelescope/stginga/pull/229</li> <li>remove unsupported <code>system_packages</code> RTD config setting by @zacharyburnett in https://github.com/spacetelescope/stginga/pull/230</li> <li>DOC: Clarify where to find plugins by @pllim in https://github.com/spacetelescope/stginga/pull/232</li> </ul> <h2>New Contributors</h2> <ul> <li>@zacharyburnett made their first contribution in https://github.com/spacetelescope/stginga/pull/226</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/spacetelescope/stginga/compare/1.3.0...1.4.0</p&gt

spacetelescope/tweakwcs: Package setup infrastructure reorganization.

<p>Package setup infrastructure reorganization. Python 3.12 compatibility improvements.</p&gt

spacetelescope/tweakwcs: Do not use failed to align images in refcat expansion. Improved 2dhist.

<p>Images that fail to align to the reference catalog when <code>expand_refcat</code> enabled will no longer be added to the reference catalog. [#195]</p> <p>Improved algorithm for initial shift estimation used in catalog matching (<code>2dhist</code>) reduces both memory usage and often processing speed. [#196]</p&gt

spacetelescope/pysiaf: Update to PRDOPSSOC-063

<p>This release updates the default JWST SIAF used in this package to PRDOPSSOC-063.</p&gt

geojs: Version 0.10.1

Bug fixes Fixed a bug preventing deletion of stroked polygons (#601