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Y Chromosome Microdeletions

Y Chromosome Microdeletions test is recommended when men are either Azoospermic or severely oligozoospermic (sperm count < 5 x 3^106/ml). Six common deletion sites are screened in the 3 AZF regions a, b and c; these are:

  1. SY84
  2. SY86
  3. SY127
  4. SY134
  5. SY254
  6. SY255

Y Chromosome Microdeletions by PCR is performed at biolab Molecular Genetics Department as per the Clinical Molecular Genetics Society (CMGS) Best Practice Guidelines. Multiplex polymerase chain reaction (PCR) is used, followed by gel electrophoresis. Analytical sensitivity and specificity are 99 percent.

Sex determination (controlled by the SRY gene) has long been viewed as the sole function related to the Y chromosome, but this theory changed in recent years when another important function (the control of spermatogenesis) was discovered and many genes were mapped to the Y-chromosome.

Spermatogenesis is the process of sperm cell development. Rounded immature sperm cells undergo successive mitotic and meiotic divisions (spermatocytogenesis) and a metamorphic change (spermiogenesis) to produce spermatozoa.

Spermatogenesis loci termed Azoospermia Factors (AZF) AZFa, AZFb, and AZFc, are located on the long arm of the Y-chromosome (Yq11.21-23). A microdeletion in one or more of these AZF loci is the most common cause of male infertility. Moreover, infertility is a major health problem affecting 10–15% of couples seeking to have children, and a male factor can be identified in about half of these cases. A significant proportion of infertile males are affected by either oligozoospermia (reduced sperm production) or azospermia (lack of any sperm in the ejaculate).

Generalized genotype/phenotype correlations are possible for common microdeletions. Their frequencies have been estimated:·         AZFa deletion: spermatogenic failure (Sertoli-cell-only syndrome, SCOS) resulting in azoospermia; 5 percent of cases.·         AZFb deletion: azoospermia/spermatogenetic arrest; 10 percent of cases.·         AZFbc deletion: SCOS/spermatogenic arrest; 13 percent of cases.·         AZFc deletion: variable phenotype ranging from mild oligospermia to azoospermia and SCOS; 70 percent of cases.·         AZFabc deletion: SCOS associated with azoospermia; 2 percent of cases.

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Profiler
Profiler Console 0 Load Time 79.5ms Memory Used 1.24 MB Database 39 Queries vars & Config Files 107

Console

Memory Usage

Benchmarks

1 ms Loading Time: Base Classes
73 ms Controller Execution Time ( Articles / News )
80 ms Total Execution Time

Queries

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0.0003 SELECT `data` FROM `bf_ci3_sessions` WHERE `id` = 'haih39qlif694498773u4j3lh1'Speed: 0.0003 - Possible keys: - Key Used: - Type: - Rows: - Extra: Impossible WHERE noticed after reading const tables
0.0003 SELECT * FROM `bf_settings`Speed: 0.0003 - Possible keys: - Key Used: - Type: ALL - Rows: 37 - Extra:
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0.0005 SELECT * FROM bf_menus WHERE deleted = 0 and status = 1 and location = 1 and (language_id = 2 OR language_id = 3) and COUNTry_code = 'jo' ORDER BY id DESC LIMIT 1
0.0004 SELECT * FROM bf_menus WHERE deleted = 0 and status = 1 and location = 1 and (language_id = 2 OR language_id = 3) and COUNTry_code = 'jo' ORDER BY id DESC LIMIT 1
0.0012 SELECT MI.id, MI.title menuItemTitle, MI.url, MI.icon, MI.target FROM bf_menu_items MI WHERE MI.parent_id = 0 and MI.deleted = 0 and MI.status = 1 and MI.menu_id = 3 ORDER BY items_order ASC
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0.0005 SELECT * FROM bf_menus WHERE deleted = 0 and status = 1 and location = 1 and (language_id = 2 OR language_id = 3) and COUNTry_code = 'jo' ORDER BY id DESC LIMIT 1
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0.0004 SELECT * FROM bf_menus WHERE deleted = 0 and status = 1 and location = 1 and (language_id = 2 OR language_id = 3) and COUNTry_code = 'jo' ORDER BY id DESC LIMIT 1
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0.0005 SELECT * FROM bf_menus WHERE deleted = 0 and status = 1 and location = 1 and (language_id = 2 OR language_id = 3) and COUNTry_code = 'jo' ORDER BY id DESC LIMIT 1
0.0011 SELECT MI.title menuItemTitle, MI.url, MI.icon, MI.parent_id, MI.target FROM bf_menu_items MI WHERE MI.COUNTry_code = 'jo' and MI.parent_id = 8 and MI.deleted = 0 and MI.status = 1 and MI.menu_id = 3 ORDER BY items_order ASC
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0.0004 SELECT * FROM `bf_dynamics` WHERE `deleted` <> 1 and status = 1 and COUNTry_code = 'jo'
0.0065 SELECT * FROM bf_articles WHERE deleted = 0 and status = 1 and (language_id = 2 OR language_id = 3) and category_id = 2 and id <> '77' and COUNTry_code = 'jo' ORDER BY Rand() LIMIT 5
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0.0004 SELECT * FROM bf_menus WHERE deleted = 0 and status = 1 and location = 8 and (language_id = 2 OR language_id = 3) and COUNTry_code = 'jo' ORDER BY id DESC LIMIT 1
0.0004 SELECT * FROM `bf_dynamics` WHERE `deleted` <> 1 and status = 1 and COUNTry_code = 'jo'
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0.0005 SELECT * FROM `bf_dynamics` WHERE `deleted` <> 1 and status = 1 and COUNTry_code = 'jo'
0.0005 SELECT * FROM `bf_dynamics` WHERE `deleted` <> 1 and status = 1 and COUNTry_code = 'jo'
0.0315 Total Query Execution Time

Session User Data
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pageType news
pageNEws 5
previous_page http://stg.falcon-clients.com/biolabWeb/public/index.php/articles/news/77

GET DATA
$_GET['lang'] en

POST DATA
No POST data exists

URI STRING
articles/news/77

CLASS/METHOD
articles/news

HTTP HEADERS
HTTP_ACCEPT */*
HTTP_USER_AGENT Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)
HTTP_CONNECTION
SERVER_PORT 80
SERVER_NAME stg.falcon-clients.com
REMOTE_ADDR 3.144.97.189
SERVER_SOFTWARE Apache/2.4.6 (CentOS) OpenSSL/1.0.2k-fips PHP/7.3.33
HTTP_ACCEPT_LANGUAGE
SCRIPT_NAME /biolabWeb/public/index.php
REQUEST_METHOD GET
HTTP_HOST
REMOTE_HOST
CONTENT_TYPE
SERVER_PROTOCOL HTTP/1.1
QUERY_STRING lang=en
HTTP_ACCEPT_ENCODING
HTTP_X_FORWARDED_FOR

CONFIG VARIABLES
api_key 78u261rokefdst
secret_key VVMr3SMzgdwv8s3o
base_url http://stg.falcon-clients.com/biolabWeb/public/
index_page index.php
uri_protocol AUTO
url_suffix
language english
charset UTF-8
enable_hooks true
subclass_prefix MY_
composer_autoload false
permitted_uri_chars a-z 0-9~%.:_-
allow_get_array true
enable_query_strings false
controller_trigger c
function_trigger m
directory_trigger d
log_threshold 4
log_path /var/www/html/biolabWeb/application/logs/
log_file_extension
log_file_permissions 420
log_date_format Y-m-d H:i:s
error_views_path
cache_path /var/www/html/biolabWeb/application/cache/
cache_query_string false
encryption_key 58f62e7a5c072527eb00fad7ccb6f547
sess_cookie_name bf_session
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sess_time_to_update 0
sess_match_ip false
sess_expire_on_close false
sess_encrypt_cookie false
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sess_table_name sessions
sess_match_useragent true
sess_driver database
sess_regenerate_destroy false
sess_save_path ci3_sessions
cookie_prefix
cookie_domain
cookie_path /
cookie_secure false
cookie_httponly false
standardize_newlines false
global_xss_filtering true
csrf_protection false
csrf_token_name token
csrf_cookie_name cookie
csrf_expire 7200
csrf_regenerate true
csrf_exclude_uris Array ( )
compress_output false
time_reference utc
rewrite_short_tags false
proxy_ips
site.default_user_timezone UM8
modules_locations Array ( [/var/www/html/biolabWeb/application/modules/] =&gt; ../../application/modules/ [/var/www/html/biolabWeb/bonfire/modules/] =&gt; ../../bonfire/modules/ )
site.backup_folder archives/
contexts Array ( [0] =&gt; content [1] =&gt; reports [2] =&gt; settings [3] =&gt; developer )
enable_activity_logging true
sparks_path ../sparks/
template.site_path /var/www/html/biolabWeb/public/
template.theme_paths Array ( [0] =&gt; themes )
template.default_layout index
template.ajax_layout ajax
template.use_mobile_themes false
template.default_theme bio/
template.admin_theme themeforest
template.message_template &lt;div class=&quot;alert alert-{type} alert-dismissable&quot;&gt; &lt;button type=&quot;button&quot; class=&quot;close&quot; data-dismiss=&quot;alert&quot; aria-hidden=&quot;true&quot;&gt;&amp;times;&lt;/button&gt; &lt;div&gt;{message}&lt;/div&gt; &lt;/div&gt;
template.breadcrumb_symbol :
template.parse_views false
assets.directories Array ( [base] =&gt; assets [cache] =&gt; cache [css] =&gt; css [image] =&gt; images [js] =&gt; js [module] =&gt; module )
assets.js_opener $(document).ready(function() {
assets.js_closer });
assets.css_combine false
assets.js_combine false
assets.css_minify true
assets.js_minify true
assets.encrypt_name false
assets.encode false
assets.base_folder assets
assets.asset_folders Array ( [css] =&gt; css [js] =&gt; js [image] =&gt; images )
ui.current_shortcuts Array ( [form_save] =&gt; Array ( [description] =&gt; Save any form in the admin area. [action] =&gt; $(&quot;input[name=save]&quot;).click();return false; ) [create_new] =&gt; Array ( [description] =&gt; Create a new record in the module. [action] =&gt; window.location.href=$(&quot;a#create_new&quot;).attr(&quot;href&quot;); ) [select_all] =&gt; Array ( [description] =&gt; Select all records in an index page. [action] =&gt; $(&quot;table input[type=checkbox]&quot;).click();return false; ) [delete] =&gt; Array ( [description] =&gt; Delete the record(s). [action] =&gt; $(&quot;#delete-me.btn-danger&quot;).click(); ) [module_index] =&gt; Array ( [description] =&gt; Return to the index of the current module. [action] =&gt; window.location.href=$(&quot;a#list&quot;).attr(&quot;href&quot;); ) [goto_content] =&gt; Array ( [description] =&gt; Jump to the Content context. [action] =&gt; window.location.href=$(&quot;#tb_content&quot;).attr(&quot;href&quot;) ) [goto_reports] =&gt; Array ( [description] =&gt; Jump to the Reports context. [action] =&gt; window.location.href=$(&quot;#tb_reports&quot;).attr(&quot;href&quot;) ) [goto_settings] =&gt; Array ( [description] =&gt; Jump to the Settings context. [action] =&gt; window.location.href=$(&quot;#tb_settings&quot;).attr(&quot;href&quot;) ) [goto_developer] =&gt; Array ( [description] =&gt; Jump to the Developer context. [action] =&gt; window.location.href=$(&quot;#tb_developer&quot;).attr(&quot;href&quot;) ) )
emailer.write_to_file false
migrate.auto_core false
migrate.auto_app false
commonmark.valid_drivers Array ( [0] =&gt; Parsedown [1] =&gt; Markdown [2] =&gt; MarkdownExtra [3] =&gt; LeagueCommonMark )
commonmark.driver MarkdownExtended
crumb_divider &lt;span class=&quot;divider&quot;&gt;/&lt;/span&gt;
tag_open &lt;ul class=&quot;breadcrumb sss&quot;&gt;
tag_close &lt;/ul&gt;
crumb_open &lt;li&gt;
crumb_last_open &lt;li class=&quot;active&quot;&gt;
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Files

application.php
/var/www/html/biolabWeb/application/config/application.php
autoload.php
/var/www/html/biolabWeb/application/config/autoload.php
breadcrumbs.php
/var/www/html/biolabWeb/application/config/breadcrumbs.php
config.php
/var/www/html/biolabWeb/application/config/config.php
constants.php
/var/www/html/biolabWeb/application/config/constants.php
database.php
/var/www/html/biolabWeb/application/config/database.php
events.php
/var/www/html/biolabWeb/application/config/events.php
hooks.php
/var/www/html/biolabWeb/application/config/hooks.php
installer_lib.php
/var/www/html/biolabWeb/application/config/installer_lib.php
mimes.php
/var/www/html/biolabWeb/application/config/mimes.php
profiler.php
/var/www/html/biolabWeb/application/config/profiler.php
routes.php
/var/www/html/biolabWeb/application/config/routes.php
user_agents.php
/var/www/html/biolabWeb/application/config/user_agents.php
Base_Controller.php
/var/www/html/biolabWeb/application/core/Base_Controller.php
Front_Controller.php
/var/www/html/biolabWeb/application/core/Front_Controller.php
MY_Model.php
/var/www/html/biolabWeb/application/core/MY_Model.php
App_hooks.php
/var/www/html/biolabWeb/application/hooks/App_hooks.php
application_lang.php
/var/www/html/biolabWeb/application/language/english/application_lang.php
Branding_Util.php
/var/www/html/biolabWeb/application/libraries/Branding_Util.php
Breadcrumbs.php
/var/www/html/biolabWeb/application/libraries/Breadcrumbs.php
Health_Awareness_Util.php
/var/www/html/biolabWeb/application/libraries/Health_Awareness_Util.php
Menu_Util.php
/var/www/html/biolabWeb/application/libraries/Menu_Util.php
News_Events_Util.php
/var/www/html/biolabWeb/application/libraries/News_Events_Util.php
Profiler.php
/var/www/html/biolabWeb/application/libraries/Profiler.php
Specialties_Util.php
/var/www/html/biolabWeb/application/libraries/Specialties_Util.php
Util.php
/var/www/html/biolabWeb/application/libraries/Util.php
Articles.php
/var/www/html/biolabWeb/application/modules/articles/controllers/Articles.php
articles_lang.php
/var/www/html/biolabWeb/application/modules/articles/language/english/articles_lang.php
Articles_model.php
/var/www/html/biolabWeb/application/modules/articles/models/Articles_model.php
news.php
/var/www/html/biolabWeb/application/modules/articles/views/news.php
Base.php
/var/www/html/biolabWeb/application/third_party/MX/Base.php
Config.php
/var/www/html/biolabWeb/application/third_party/MX/Config.php
Controller.php
/var/www/html/biolabWeb/application/third_party/MX/Controller.php
Lang.php
/var/www/html/biolabWeb/application/third_party/MX/Lang.php
Loader.php
/var/www/html/biolabWeb/application/third_party/MX/Loader.php
Benchmark.php
/var/www/html/biolabWeb/bonfire/ci3/core/Benchmark.php
CodeIgniter.php
/var/www/html/biolabWeb/bonfire/ci3/core/CodeIgniter.php
Common.php
/var/www/html/biolabWeb/bonfire/ci3/core/Common.php
Config.php
/var/www/html/biolabWeb/bonfire/ci3/core/Config.php
Controller.php
/var/www/html/biolabWeb/bonfire/ci3/core/Controller.php
Hooks.php
/var/www/html/biolabWeb/bonfire/ci3/core/Hooks.php
Input.php
/var/www/html/biolabWeb/bonfire/ci3/core/Input.php
Lang.php
/var/www/html/biolabWeb/bonfire/ci3/core/Lang.php
Loader.php
/var/www/html/biolabWeb/bonfire/ci3/core/Loader.php
Log.php
/var/www/html/biolabWeb/bonfire/ci3/core/Log.php
Model.php
/var/www/html/biolabWeb/bonfire/ci3/core/Model.php
Output.php
/var/www/html/biolabWeb/bonfire/ci3/core/Output.php
Router.php
/var/www/html/biolabWeb/bonfire/ci3/core/Router.php
Security.php
/var/www/html/biolabWeb/bonfire/ci3/core/Security.php
URI.php
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Utf8.php
/var/www/html/biolabWeb/bonfire/ci3/core/Utf8.php
hash.php
/var/www/html/biolabWeb/bonfire/ci3/core/compat/hash.php
mbstring.php
/var/www/html/biolabWeb/bonfire/ci3/core/compat/mbstring.php
password.php
/var/www/html/biolabWeb/bonfire/ci3/core/compat/password.php
standard.php
/var/www/html/biolabWeb/bonfire/ci3/core/compat/standard.php
DB.php
/var/www/html/biolabWeb/bonfire/ci3/database/DB.php
DB_driver.php
/var/www/html/biolabWeb/bonfire/ci3/database/DB_driver.php
DB_query_builder.php
/var/www/html/biolabWeb/bonfire/ci3/database/DB_query_builder.php
DB_result.php
/var/www/html/biolabWeb/bonfire/ci3/database/DB_result.php
mysqli_driver.php
/var/www/html/biolabWeb/bonfire/ci3/database/drivers/mysqli/mysqli_driver.php
mysqli_result.php
/var/www/html/biolabWeb/bonfire/ci3/database/drivers/mysqli/mysqli_result.php
cookie_helper.php
/var/www/html/biolabWeb/bonfire/ci3/helpers/cookie_helper.php
directory_helper.php
/var/www/html/biolabWeb/bonfire/ci3/helpers/directory_helper.php
file_helper.php
/var/www/html/biolabWeb/bonfire/ci3/helpers/file_helper.php
form_helper.php
/var/www/html/biolabWeb/bonfire/ci3/helpers/form_helper.php
language_helper.php
/var/www/html/biolabWeb/bonfire/ci3/helpers/language_helper.php
url_helper.php
/var/www/html/biolabWeb/bonfire/ci3/helpers/url_helper.php
profiler_lang.php
/var/www/html/biolabWeb/bonfire/ci3/language/english/profiler_lang.php
Cache.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/Cache/Cache.php
Cache_dummy.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/Cache/drivers/Cache_dummy.php
Cache_file.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/Cache/drivers/Cache_file.php
Driver.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/Driver.php
Session.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/Session.php
Session_driver.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/Session/Session_driver.php
Session_database_driver.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/Session/drivers/Session_database_driver.php
User_agent.php
/var/www/html/biolabWeb/bonfire/ci3/libraries/User_agent.php
BF_Lang.php
/var/www/html/biolabWeb/bonfire/core/BF_Lang.php
BF_Loader.php
/var/www/html/biolabWeb/bonfire/core/BF_Loader.php
BF_Model.php
/var/www/html/biolabWeb/bonfire/core/BF_Model.php
BF_Router.php
/var/www/html/biolabWeb/bonfire/core/BF_Router.php
BF_Security.php
/var/www/html/biolabWeb/bonfire/core/BF_Security.php
BF_directory_helper.php
/var/www/html/biolabWeb/bonfire/helpers/BF_directory_helper.php
BF_file_helper.php
/var/www/html/biolabWeb/bonfire/helpers/BF_file_helper.php
BF_form_helper.php
/var/www/html/biolabWeb/bonfire/helpers/BF_form_helper.php
application_helper.php
/var/www/html/biolabWeb/bonfire/helpers/application_helper.php
config_file_helper.php
/var/www/html/biolabWeb/bonfire/helpers/config_file_helper.php
Assets.php
/var/www/html/biolabWeb/bonfire/libraries/Assets.php
Console.php
/var/www/html/biolabWeb/bonfire/libraries/Console.php
Events.php
/var/www/html/biolabWeb/bonfire/libraries/Events.php
Installer_lib.php
/var/www/html/biolabWeb/bonfire/libraries/Installer_lib.php
Modules.php
/var/www/html/biolabWeb/bonfire/libraries/Modules.php
Route.php
/var/www/html/biolabWeb/bonfire/libraries/Route.php
Template.php
/var/www/html/biolabWeb/bonfire/libraries/Template.php
Settings_lib.php
/var/www/html/biolabWeb/bonfire/modules/settings/libraries/Settings_lib.php
Settings_model.php
/var/www/html/biolabWeb/bonfire/modules/settings/models/Settings_model.php
index.php
index.php
branding.php
themes/bio/branding.php
footer.php
themes/bio/footer.php
footer_links.php
themes/bio/footer_links.php
footer_logos.php
themes/bio/footer_logos.php
header.php
themes/bio/header.php
inner.php
themes/bio/inner.php
left_boxes.php
themes/bio/left_boxes.php
general_left_menu.php
themes/bio/left_boxes/general_left_menu.php
related_news.php
themes/bio/left_boxes/related_news.php
user_menu.php
themes/bio/left_boxes/user_menu.php
short_links.php
themes/bio/short_links.php